Gene_locus Report for: mouse-Ces4a Mus musculus (Mouse) Carboxylesterase 4A (Ces4a) Carboxylesterase 8 (Ces8) pI 6.1 esterase (ES-10) ES-HVEL
Comment
on Chromosome 8 Relationship
(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) cellular organisms: N E > Eukaryota: N E > Opisthokonta: N E > Metazoa: N E > Eumetazoa: N E > Bilateria: N E > Deuterostomia: N E > Chordata: N E > Craniata: N E > Vertebrata: N E > Gnathostomata: N E > Teleostomi: N E > Euteleostomi: N E > Sarcopterygii: N E > Dipnotetrapodomorpha: N E > Tetrapoda: N E > Amniota: N E > Mammalia: N E > Theria: N E > Eutheria: N E > Boreoeutheria: N E > Euarchontoglires: N E > Glires: N E > Rodentia: N E > Myomorpha: N E > Muroidea: N E > Muridae: N E > Murinae: N E > Mus [genus]: N E > Mus [subgenus]: N E > Mus musculus: N E A85-EsteraseD-FGH :
mouse-ES10 Mus musculus esterase 10 .
ABHD6-Lip :
mouse-ABHD6 Mus musculus (Mouse) Monoacylglycerol lipase ABHD6 .
ABHD8 :
mouse-Abhd8 Mus musculus Q9JMF5-Abhd8 (Mouse) epoxide hydrolase (EC 3.3.2.3) .
ABHD10 :
mouse-abhda .
ABHD11-Acetyl_transferase :
mouse-Abhd11 Mus musculus (Mouse) Abhydrolase domain-containing protein 11 Williams-Beuren syndrome chromosomal region 21 protein .
ABHD12-PHARC :
mouse-abd12 Mus musculus (Mouse) abhydrolase domain-containing protein 12 protein c20orf22 CT022 (fragment) ,
mouse-g3uzn6 Mus musculus (Mouse) Protein Abhd12b .
ABHD13-BEM46 :
mouse-Q80UX8 Mus musculus (Mouse) 1110065l07rik protein flj14906 fis Alpha/beta hydrolase domain-containing protein 13 .
ABHD16 :
mouse-Abhd16a Mus musculus (Mouse) Phosphatidylserine lipase ABHD16A, bat5 (hla-b-associated transcript 5) (ng26 protein) ,
mouse-Abhd16b Mus musculus (Mouse) similar to chromosome 20 open reading frame 135 .
ABHD17-depalmitoylase :
mouse-q7m759 Mus musculus (Mouse) cgi67 serine protease precursor ,
mouse-Q8VCV1 Mus musculus (Mouse) hypothetical protein ,
mouse-Q99JW1 Mus musculus (Mouse) similar to cgi-67 protein AB17A .
ABHD18 :
mouse-Q8C1A9 Mus musculus (Mouse)3110057O12RIK Hypothetical alpha/beta-Hydrolases/putative DNA-binding domain .
abh_upf0017 :
mouse-ABH15 Mus musculus (Mouse) alpha/beta-hydrolases domain-containing protein 15 ,
mouse-abhd1 Mus musculus (Mouse) lung alpha/beta hydrolase 1 (Labh1-pending) ,
mouse-abhd3 Mus musculus (Mouse) lung alpha/beta hydrolase fold protein 3 ,
mouse-ABHD2 Mus musculus (Mouse) alpha/beta hydrolase-2 fold protein 2210009N18RIK .
ACHE :
mouse-ACHE .
Acidic_Lipase :
mouse-1lipg Mus musculus (Mouse) (EC 3.1.1.3) (Gastric lipase) (GL) 2310051b21rik protein ,
mouse-1llip Mus musculus (C57 Black/6X CBA) LAL mRNA for lysosomal acid lipase ,
mouse-LIPK Mus musculus (Mouse) LIPK Lipl2 weakly similar to triacylglycerol lipase ,
mouse-LIPM Mus musculus (Mouse) LIPM Lipm Lipl3 riken cdna 4632427c23 gene ,
mouse-LIPN Mus musculus (Mouse) lipase-like, ab-hydrolase domain containing 3 (fragment) ,
mouse-Lipo1 Mus musculus (Mouse) lipase, gastric (EC 3.1.1.3) (gastric lipase) (gl) ,
mouse-Lipo2 Mus musculus (Mouse) Lipo2 Lipase ,
mouse-Lipo4 Mus musculus (Mouse) Lipo4 Lipase .
ACPH_Peptidase_S9 :
mouse-apeh Mus musculus (Mouse) hydrolase) (aph) (acylaminoacyl-peptidase) .
Acyl-CoA_Thioesterase :
mouse-acnt1 Mus musculus (Mouse) Acyl-coenzyme A amino acid N-acyltransferase 1 ,
mouse-acot1 Mus musculus (Mouse) hydrolase) ACOT1 (cte-I) cytosolic long chain Acyl-CoA thioesterase ,
mouse-acot2 Mus musculus (Mouse) (EC 3.1.2.2) very-long-chain Acyl-CoA thioesterase (MTE-I) ACOT2 ,
mouse-acot3 Mus musculus (Mouse) (peroxisomal long-chain Acyl-CoA thioesterase 2) (pte-IA) (EC 3.1.2.2) ,
mouse-acot4 Mus musculus (Mouse) peroxisomal long chain Acyl-CoA thioesterase Ib (pte-Ib) (pte-2b) ,
mouse-acot5 Mus musculus (Mouse) (peroxisomal cytosolic Acyl-CoA thioesterase Ic) ,
mouse-BAAT Mus musculus (Mouse) bile acid CoA: amino acid n-acyltransferase (EC 3.1.2.2) ,
mouse-ACOT6 Mus musculus (Mouse)acyl-CoA thioesterase 6 (EC 3.1.2.2). Weakly similar to peroxisomal acyl-coenzyme A thioester hydrolase2 ,
mouse-Q8BGG9 Mus musculus (Mouse) Similar to bile acid coenzyme A: amino acid N-acyltransferase .
Arb2_FAM172A :
mouse-f172a Mus musculus (Mouse). Cotranscriptional regulator FAM172A .
Arylacetamide_deacetylase :
mouse-adcl3 Mus musculus (Mouse) Arylacetamide deacetylase-like 3 ,
mouse-adcl4 Mus musculus (Mouse) Arylacetamide deacetylase-like 4 Hypothetical esterase/lipase/thioesterase family active site containing protein ,
mouse-aryla Mus musculus (Mouse) arylacetamide deacetylase and 5033417e09rik protein ,
mouse-Q8BLF1 Mus musculus (Mouse) KIAA1363 NCEH1 neutral cholesterol ester hydrolase 1 B230106I24RIK ,
mouse-b1avu7 Mus musculus (Mouse). Uncharacterized protein ,
mouse-b2rwd2 Mus musculus (Mouse). Arylacetamide deacetylase-like 2 ,
mouse-j3qpi0 Mus musculus (Mouse). Uncharacterized protein ,
mouse-w4vsp6 Mus musculus (Mouse). MCG67716 .
BCHE :
mouse-BCHE Mus musculus mRNA for butyrylcholinesterase .
Carboxypeptidase_S10 :
mouse-CPMac Mus musculus RIKEN 4933436L16RIK CPMac ,
mouse-Ppgb ,
mouse-RISC Mus musculus RISC retinoid-inducible serine carboxypeptidase HSCP1 (serine carboxypeptidase 1) .
Carb_B_Chordata :
mouse-cauxin Mus musculus (Mouse) est5a (Ces5a) est7 (Ces7) carboxylesterase-like urinary excreted protein ,
mouse-Ces1a Mus musculus Ces1a LOC2445 Q5FWH4 ,
mouse-Ces1b Mus musculus (Mouse) Putative uncharacterized protein Gm5158 ,
mouse-Ces1c Mus musculus mRNA for carboxylesterase, Ces1c lung surfactant convertase, Liver carboxylesterase N, PES-N clone MGC:18575 ,
mouse-Ces1d Mus musculus (Mouse) triacylglycerol hydrolase (tgh) Fatty acid ethyl ester synthase Carboxylesterase 3 (EC 3.1.1.1) ,
mouse-Ces1e Mus musculus esterase-22 (egasyn) Es-22 E.R.-targeting prot. of beta-glucuronidase ,
mouse-Ces1f Mus musculus (Mouse) carboxylesterase ML1, CESmML1 61.6 kda protein ES-4 (EC 3.1.1.1) ,
mouse-Ces1g Mus musculus Ces1g EST1 RIKEN 2cxes mRNA for carboxylesterase ,
mouse-Ces1h Mus musculus Ces1h RIKEN cDNA 2310039D24 gene (2310039D24Rik),XP_134476 ,
mouse-Ces2a Mus musculus (Mouse) Protein Ces2a Ces6 carboxylesterase 6 (Intestine, liver) AI266984 ,
mouse-Ces2b Mus musculus (Mouse) Ces2b hypothetical protein bc015286 ,
mouse-Ces2c ,
mouse-Ces2d-ps Mus musculus (Mouse) Ces2d-ps carboxylesterase 2D, pseudogene ,
mouse-Ces2e Mus musculus Ces2e Ces5 carboxylesterase, Pyrethroid hydrolase ,
mouse-Ces2f Mus musculus (Mouse) Ces2f Uncharacterized protein ,
mouse-Ces2g Mus musculus (Mouse) hypothetical 62.7 kda protein ,
mouse-Ces2h Mus musculus Ces2h carboxylesterase 2 isoform 1 ,
mouse-Ces3a Mus musculus Ces3a liver carboxylesterase esterase 31 Es31 ,
mouse-Ces3b Mus musculus (Mouse) Liver carboxylesterase 31-like, Es31L .
CGI-58_ABHD5_ABHD4 :
mouse-abhd4 Mus musculus (Mouse) abhydrolase domain-containing protein 4 similar to hypothetical protein flj12816 ,
mouse-abhd5 Mus musculus (Mouse) cgi-58 RIKEN AK004873 gene .
Cholesterol_esterase :
mouse-pches Mus musculus pancreatic/mammary gland cholesterol esterase .
CIB-CCG1-interacting-factor-B :
mouse-c1ib Mus musculus (Mouse) ccg1-interacting factor b ,
mouse-Dorz1 Mus musculus (Mouse)1110013B16RIK Dorz1 similar to dkfzp564o243 protein .
CMBL :
mouse-CMBL Mus musculus (Mouse) Carboxymethylenebutenolidase homolog .
DPP4N_Peptidase_S9 :
mouse-dpp4 M.musculus mRNA for dipeptidyl peptidase IV ,
mouse-DPP6 Mus musculus (Mouse) dipeptidyl aminopeptidase-like protein 6 (fragment) ,
mouse-dpp8 Mus musculus RIKEN dpp8 ,
mouse-dpp9 Mus musculus (Mouse) dipeptidyl peptidase 9 homolog mflj00334 protein ,
mouse-dpp10 Mus musculus DPP-10 Dipeptidyl peptidase IV-related protein RIKEN cDNA 6430601K09 gene (6430601K09Rik), mRNA ,
mouse-FAP Mus musculus (Mouse) fibroblast activation protein .
Duf_676 :
mouse-F135A Mus musculus (Mouse) hypothetical Esterase/lipase/thioesterase family active site containing protein ,
mouse-Q9DAI6 Mus musculus (Mouse) family active site containing protein, similarity 135, member B .
Duf_726 :
mouse-tmco4 Mus musculus (Mouse) Transmembrane and coiled-coil domain-containing protein 4 .
Duf_829 :
mouse-tmm53 Mus musculus (Mouse) Transmembrane protein 53 .
Epoxide_hydrolase :
mouse-EPHX1 Mus musculus (Mouse) epoxide hydrolase mEH (EC 3.3.2.3) ,
mouse-ephx3 Mus musculus (Mouse) Abhd9 ephx3 Epoxide_hydrolase sequence ,
mouse-ephx4 Mus musculus (Mouse) epoxide hydrolase-related protein ,
mouse-hyes .
FSH1 :
mouse-OVCA2 Mus musculus (Mouse) 2310011m22rik protein (ovca2) .
Hepatic_Lipase :
mouse-1hlip Mus musculus (Mouse), Mus spretus (Western Mediterranean mouse) (Algerian mouse) hepatic triacylglycerol lipase .
Hormone-sensitive_lipase_like :
mouse-hslip Mus musculus mRNA for hormone sensitive lipase .
Hydrolase_RBBP9_YdeN :
mouse-rbbp9 Mus musculus (Mouse), Mus spretus (Western Mediterranean mouse), (Retinoblastoma-binding protein 9 protein) B5T overexpressed gene protein (bog protein) .
Kynurenine-formamidase :
mouse-KFA Mus musculus Kynurenine formamidase (EC 3.5.1.9) Afmid Ammd cDNA 9030621K19 gene (9030621K19Rik) .
LIDHydrolase :
mouse-Ldah Mus musculus (Mouse) lipid droplet-associated hydrolase (LDAH) C2orf43 CB043 UPF0554 .
Lipase_3 :
mouse-DGLB Mus musculus (Mouse) Daglb Sn1-specific diacylglycerol lipase beta 64.9 kda protein ,
mouse-q6wqj1 Mus musculus (Mouse) Dagla neural stem cell-derived dendrite regulator DAGLA .
Lipoprotein_Lipase :
mouse-Lipg Mus musculus (Mouse) Lipg endothelial lipase ,
mouse-lipli Mus musculus lipoprotein lipase .
LYsophospholipase_carboxylesterase :
mouse-lypl1 Mus musculus (Mouse) lysophospholipase-like protein 1 (EC 3.1.2.-) 26.3 kda protein ,
mouse-lypla1 Mus musculus lysophospholipase 1 (Lypla1)(lysopla I), mRNA ,
mouse-lypla2 Mus musculus lysophospholipase 2 (Lypla2), mRNA .
Maspardin-ACP33-SPG21_like :
mouse-SPG21 Mus musculus (Mouse) hypothetical Maspardin-ACP33-SPG21 Spg21 Spastic paraplegia 21 homolog (Human) .
MEST-like :
mouse-MEST Mus musculus Mouse and Mus musculus molossinus (Japanese house mouse) Mesoderm-specific transcript protein .
Monoglyceridelipase_lysophospholip :
mouse-MGLL Mus musculus (Mouse) monoglyceride lipase (EC 3.1.1.23) .
Ndr_family :
mouse-ndr1 Mus musculus (Mouse) ndr1 ,
mouse-ndr2 ,
mouse-ndr3 Mus musculus (Mouse) ndrg3 protein (ndr3 protein) ,
mouse-ndr4 Mus musculus (Mouse) NDRG4 ndrg4 protein mkiaa1180 .
Neuroligin :
mouse-1neur ,
mouse-2neur ,
mouse-3neur ,
mouse-4neur Mus musculus (Mouse) neuroligin 4 .
NLS3-Tex30 :
mouse-Kansl3 Mus musculus (Mouse) Q8C0P9 4632411B12RIK serum inhibited-related protein homolog ,
mouse-Tex30 Mus musculus (Mouse) Tex30 Testis-expressed sequence 30 protein, C13orf27 homolog .
PAF-Acetylhydrolase :
mouse-paf2 Mus musculus (Mouse) similar to platelet-activating factor acetylhydrolase 2 (40 kda) ,
mouse-pafa Mus musculus plasma PAF acetylhydrolase .
Palmitoyl-protein_thioesterase :
mouse-ppt Mus musculus (Mouse) palmitoyl-protein thioesterase ,
mouse-PPT2 Mus musculus (Mouse) palmitoyl-protein thioesterase 2 .
Pancreatic_lipase :
mouse-1plip Mus musculus RIKEN Pancreatic lipase ,
mouse-1plrp Mus musculus (Mouse) pancreatic lipase related protein 1 ,
mouse-LIPR2 Mus musculus mRNA for cytotoxic T lymphocyte lipase .
PC-sterol_acyltransferase :
mouse-C87498 Mus musculus (Mouse) similar to LCAT-like lysophospholipase (llpl) ,
mouse-lcat Mus musculus mRNA for phosphatidylcholine-sterol acyltransferase ( lecithin: cholesterol acyltransferase) .
Pectinacetylesterase-Notum :
mouse-notum Mus musculus (Mouse) Protein notum homolog .
PGAP1 :
mouse-q3uuq7 Mus musculus (Mouse) gpi deacylase full insert sequence. (fragment) ,
mouse-srac1 Mus musculus (Mouse) Protein SERAC1 .
Phospholipase :
mouse-LIPH Mus musculus (Mouse) similar to lacrimal lipase ,
mouse-psplip Mus musculus Similar to phosphatidylserine-specific phospholipase A1alpha ,
mouse-f6yqt7 Mus musculus (Mouse). Lipase, member I .
PPase_methylesterase_euk :
mouse-PPME1 Mus musculus (Mouse) similar to protein phosphatase methylesterase-1 .
Prolylcarboxypeptidase :
mouse-dpp2 Mus musculus (Mouse) Dipeptidyl aminopeptidase II Dipeptidyl peptidase 7 ,
mouse-pcp Mus musculus (Mouse) prcp protein 2510048k03rik protein prolylcarboxypeptidase ,
mouse-tssp Mus musculus (Mouse) thymus-specific serine protease precursor (EC 3.4.-.-) ottmusp00000000643 .
S9N_PPCE_Peptidase_S9 :
mouse-ppce Mus musculus (Mouse) (PE) prolyl endopeptidase POP PREP .
S9N_PREPL_Peptidase_S9 :
mouse-Q8C167 Mus musculus (Mouse) PERLP unknown (protein for mgc:7980) mkiaa0436 .
SERHL :
mouse-SERHL Mus musculus (Mouse) serine hydrolase-like protein 0610008b10rik protein and isoforms shl-2 (1110019m09rik protein) .
Thioesterase :
mouse-AI607300 Mus musculus (Mouse) hydrolase (mch) SAST ,
mouse-FASN Mus musculus (Mouse) fatty acid synthase FAS oleoyl-[acyl-carrier-protein] hydrolase (EC 3.1.2.14) Thioesterase domain .
Thyroglobulin :
mouse-thyro Mus musculus thyroglobulin cDNA .
Valacyclovir-hydrolase :
mouse-bphl Mus musculus (Mouse) biphenyl hydrolase-like, breast epithelial mucin-assoc AG BPHL (mcnaa), Valacyclovir hydrolase 2010012d11 rik protein Warning: This entry is a compilation of different species or line or strain with more than 90% amino acide identity. You can
retrieve all strain data
(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) Mus musculus molossinus:
N ,
E .
Molecular evidence
Database
No mutation No structure No kinetic No Substrate No inhibitor
Sequence
Graphical view for this peptide sequence: mouse-Ces4a Colored MSA for Carb_B_Chordata (raw)
MKWILGLSLTLCLVVQTALGALHTKEPLLITKHGILQGKQVHVGDTPIQV
FLGIPFSKPPVGTRRFAPPEPPLPWNGIRDATTYPPSCLQESWGQILSMY
LNTRKQYKWLHFSEDCLYLNVYAPVLAPGAPLLPVMVWFPGGAFLAGSAS
TYEGSELAARGKVVLVFLQYRLGILGFFSTGNSHARGNWGLLDQIAALRW
VQENIEAFGGDPDSVTLFGQSAGAMSVSGLMVSPLAQGLFHQAISQSGTA
VLKAFITPDPLTSAKKIAHLAGCDHNSTKVMVECLRSLSAEEVTLVSKRM
SFFQANSHKDPKEIVWFLSPVVDGVVFPEDPVVLLTRGQVKPVPYLLGVN
NAEFEWNLPFLMKIQLNQRMMNQTNINKILWSFNVLLNITKEQVPVVARE
YLNDAISNHDWKMFRNRLIDLIGDATFVYATLQAARYHRDAGSPVYLYEF
KHHASSGIIIKPYNGADHGDELSYLFGSPFSKGSSAGEEKEFSLQMMKYW
ANFAHTGNPNGEKLPYWPRFDKDEKYLQLDFDTRVGVKLKEKKMAFWSQL
RQSQKP
Legend
This sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA
M K W I L G L S L T L C L V V Q T A L G A L H T K E P L L I T K H G I L Q G K Q V H V G D T P I Q V F L G I P F S K P P V G T R R F A P P E P P L P W N G I R D A T T Y P P S C L Q E S W G Q I L S M Y L N T R K Q Y K W L H F S E D C L Y L N V Y A P V L A P G A P L L P V M V W F P G G A F L A G S A S T Y E G S E L A A R G K V V L V F L Q Y R L G I L G F F S T G N S H A R G N W G L L D Q I A A L R W V Q E N I E A F G G D P D S V T L F G Q S A G A M S V S G L M V S P L A Q G L F H Q A I S Q S G T A V L K A F I T P D P L T S A K K I A H L A G C D H N S T K V M V E C L R S L S A E E V T L V S K R M S F F Q A N S H K D P K E I V W F L S P V V D G V V F P E D P V V L L T R G Q V K P V P Y L L G V N N A E F E W N L P F L M K I Q L N Q R M M N Q T N I N K I L W S F N V L L N I T K E Q V P V V A R E Y L N D A I S N H D W K M F R N R L I D L I G D A T F V Y A T L Q A A R Y H R D A G S P V Y L Y E F K H H A S S G I I I K P Y N G A D H G D E L S Y L F G S P F S K G S S A G E E K E F S L Q M M K Y W A N F A H T G N P N G E K L P Y W P R F D K D E K Y L Q L D F D T R V G V K L K E K K M A F W S Q L R Q S Q K P
References
Title: Lineage-specific biology revealed by a finished genome assembly of the mouseChurch DM , Goodstadt L , Hillier LW , Zody MC , Goldstein S , She X , Bult CJ , Agarwala R , Cherry JL and Ponting CP <21 more author(s)> Church DM , Goodstadt L , Hillier LW , Zody MC , Goldstein S , She X , Bult CJ , Agarwala R , Cherry JL , DiCuccio M , Hlavina W , Kapustin Y , Meric P , Maglott D , Birtle Z , Marques AC , Graves T , Zhou S , Teague B , Potamousis K , Churas C , Place M , Herschleb J , Runnheim R , Forrest D , Amos-Landgraf J , Schwartz DC , Cheng Z , Lindblad-Toh K , Eichler EE , Ponting CP (- 21) Ref: PLoS Biol, 7 :e1000112, 2009 : PubMed Abstract ESTHER: Church_2009_PLoS.Biol_7_E1000112 PubMedSearch: Church 2009 PLoS.Biol 7 E1000112 PubMedID: 19468303 Gene_locus related to this paper: mouse-1neur ,
mouse-2neur ,
mouse-abd12 ,
mouse-abhd3 ,
mouse-abhd5 ,
mouse-acnt1 ,
mouse-adcl3 ,
mouse-bphl ,
mouse-c1ib ,
mouse-cauxin ,
mouse-Ces1a ,
mouse-Ces1b ,
mouse-Ces1c ,
mouse-Ces1e ,
mouse-Ces1h ,
mouse-Ces2a ,
mouse-Ces2c ,
mouse-Ces2f ,
mouse-Ces2g ,
mouse-Ces2h ,
mouse-Ces3b ,
mouse-Ces4a ,
mouse-CMBL ,
mouse-Dorz1 ,
mouse-DPP6 ,
mouse-dpp10 ,
mouse-ephx4 ,
mouse-g3uzn6 ,
mouse-KFA ,
mouse-LIPN ,
mouse-Lipo2 ,
mouse-Lipo4 ,
mouse-MEST ,
mouse-ndr1 ,
mouse-ndr4 ,
mouse-notum ,
mouse-q3uuq7 ,
mouse-Q8C1A9 ,
mouse-Q9DAI6 ,
mouse-SERHL ,
mouse-Tex30 ,
mouse-thyro ,
mouse-tmco4 ,
mouse-b1avu7 ,
mouse-b2rwd2 ,
mouse-j3qpi0 ,
mouse-w4vsp6 ,
mouse-f172a ,
mouse-f6yqt7 Abstract
The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non-protein-coding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not.
Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)Gerhard DS , Wagner L , Feingold EA , Shenmen CM , Grouse LH , Schuler G , Klein SL , Old S , Rasooly R and Malek J <104 more author(s)> Gerhard DS , Wagner L , Feingold EA , Shenmen CM , Grouse LH , Schuler G , Klein SL , Old S , Rasooly R , Good P , Guyer M , Peck AM , Derge JG , Lipman D , Collins FS , Jang W , Sherry S , Feolo M , Misquitta L , Lee E , Rotmistrovsky K , Greenhut SF , Schaefer CF , Buetow K , Bonner TI , Haussler D , Kent J , Kiekhaus M , Furey T , Brent M , Prange C , Schreiber K , Shapiro N , Bhat NK , Hopkins RF , Hsie F , Driscoll T , Soares MB , Casavant TL , Scheetz TE , Brown-stein MJ , Usdin TB , Toshiyuki S , Carninci P , Piao Y , Dudekula DB , Ko MS , Kawakami K , Suzuki Y , Sugano S , Gruber CE , Smith MR , Simmons B , Moore T , Waterman R , Johnson SL , Ruan Y , Wei CL , Mathavan S , Gunaratne PH , Wu J , Garcia AM , Hulyk SW , Fuh E , Yuan Y , Sneed A , Kowis C , Hodgson A , Muzny DM , McPherson J , Gibbs RA , Fahey J , Helton E , Ketteman M , Madan A , Rodrigues S , Sanchez A , Whiting M , Madari A , Young AC , Wetherby KD , Granite SJ , Kwong PN , Brinkley CP , Pearson RL , Bouffard GG , Blakesly RW , Green ED , Dickson MC , Rodriguez AC , Grimwood J , Schmutz J , Myers RM , Butterfield YS , Griffith M , Griffith OL , Krzywinski MI , Liao N , Morin R , Palmquist D , Petrescu AS , Skalska U , Smailus DE , Stott JM , Schnerch A , Schein JE , Jones SJ , Holt RA , Baross A , Marra MA , Clifton S , Makowski KA , Bosak S , Malek J (- 104) Ref: Genome Res, 14 :2121, 2004 : PubMed Abstract ESTHER: Gerhard_2004_Genome.Res_14_2121 PubMedSearch: Gerhard 2004 Genome.Res 14 2121 PubMedID: 15489334 Gene_locus related to this paper: human-AFMID ,
human-CES4A ,
human-CES5A ,
human-NOTUM ,
human-SERAC1 ,
human-SERHL2 ,
human-TMEM53 ,
mouse-acot1 ,
mouse-adcl4 ,
mouse-Ces2f ,
mouse-Ces4a ,
mouse-notum ,
mouse-q6wqj1 ,
mouse-Q9DAI6 ,
mouse-rbbp9 ,
mouse-SERHL ,
mouse-srac1 ,
mouse-tmm53 ,
rat-abhd6 ,
rat-abhda ,
rat-abhea ,
rat-abheb ,
rat-Ldah ,
rat-cd029 ,
rat-estd ,
rat-Kansl3 ,
rat-nceh1 ,
ratno-acph ,
ratno-CMBL ,
mouse-b2rwd2 ,
rat-b5den3 ,
rat-ab17c Abstract
The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.
Title: A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genomeMural RJ , Adams MD , Myers EW , Smith HO , Miklos GL , Wides R , Halpern A , Li PW , Sutton GG and Stephenson LD <169 more author(s)> Mural RJ , Adams MD , Myers EW , Smith HO , Miklos GL , Wides R , Halpern A , Li PW , Sutton GG , Nadeau J , Salzberg SL , Holt RA , Kodira CD , Lu F , Chen L , Deng Z , Evangelista CC , Gan W , Heiman TJ , Li J , Li Z , Merkulov GV , Milshina NV , Naik AK , Qi R , Shue BC , Wang A , Wang J , Wang X , Yan X , Ye J , Yooseph S , Zhao Q , Zheng L , Zhu SC , Biddick K , Bolanos R , Delcher AL , Dew IM , Fasulo D , Flanigan MJ , Huson DH , Kravitz SA , Miller JR , Mobarry CM , Reinert K , Remington KA , Zhang Q , Zheng XH , Nusskern DR , Lai Z , Lei Y , Zhong W , Yao A , Guan P , Ji RR , Gu Z , Wang ZY , Zhong F , Xiao C , Chiang CC , Yandell M , Wortman JR , Amanatides PG , Hladun SL , Pratts EC , Johnson JE , Dodson KL , Woodford KJ , Evans CA , Gropman B , Rusch DB , Venter E , Wang M , Smith TJ , Houck JT , Tompkins DE , Haynes C , Jacob D , Chin SH , Allen DR , Dahlke CE , Sanders R , Li K , Liu X , Levitsky AA , Majoros WH , Chen Q , Xia AC , Lopez JR , Donnelly MT , Newman MH , Glodek A , Kraft CL , Nodell M , Ali F , An HJ , Baldwin-Pitts D , Beeson KY , Cai S , Carnes M , Carver A , Caulk PM , Center A , Chen YH , Cheng ML , Coyne MD , Crowder M , Danaher S , Davenport LB , Desilets R , Dietz SM , Doup L , Dullaghan P , Ferriera S , Fosler CR , Gire HC , Gluecksmann A , Gocayne JD , Gray J , Hart B , Haynes J , Hoover J , Howland T , Ibegwam C , Jalali M , Johns D , Kline L , Ma DS , MacCawley S , Magoon A , Mann F , May D , McIntosh TC , Mehta S , Moy L , Moy MC , Murphy BJ , Murphy SD , Nelson KA , Nuri Z , Parker KA , Prudhomme AC , Puri VN , Qureshi H , Raley JC , Reardon MS , Regier MA , Rogers YH , Romblad DL , Schutz J , Scott JL , Scott R , Sitter CD , Smallwood M , Sprague AC , Stewart E , Strong RV , Suh E , Sylvester K , Thomas R , Tint NN , Tsonis C , Wang G , Williams MS , Williams SM , Windsor SM , Wolfe K , Wu MM , Zaveri J , Chaturvedi K , Gabrielian AE , Ke Z , Sun J , Subramanian G , Venter JC , Pfannkoch CM , Barnstead M , Stephenson LD (- 169) Ref: Science, 296 :1661, 2002 : PubMed Abstract ESTHER: Mural_2002_Science_296_1661 PubMedSearch: Mural 2002 Science 296 1661 PubMedID: 12040188 Gene_locus related to this paper: mouse-ABH15 ,
mouse-Ces3b ,
mouse-Ces4a ,
mouse-dpp4 ,
mouse-FAP ,
mouse-Lipg ,
mouse-Q8C1A9 ,
mouse-rbbp9 ,
mouse-SERHL ,
mouse-SPG21 ,
mouse-w4vsp6 Abstract
The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.
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