RetrogeneDB ID: | retro_ecab_25 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 2:60692403..60694575(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000002189 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSECAG00000023845 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_25
ATGAGGATCACACTCCTGATACACTGGCTTGCAGTGTTTCTGTCCTCCTCTGGACACATGTGGCCTGAGAACCCCCAGTA
TCACAGTCCCCCAGAAGTGGTGATTCCCTTGAAGTTACCTCGTACTGGAAGAGGCATGAAACCTCCAGGCATGCTCTCTT
ACAGCCTGCATTTTGGAGGCAAGAGACATGTTGTCCATCTGAGGGTCAAGAAGCATTTGCTGTCTAGACACCTTCCAGTG
TTCACCTACACAGACCAGGGTGCTCTCCTTGAAGAAAAGCCTTTTGTTCAGAATGATTGCTACTATCATGGTTATGTGGA
AGGGGACCTGGAATCCCTGGTTGCCCTCAGTACCTGTTCTGGTGGATTTCAAGGATTGTTACAGATAAATAGCATTGTTT
ATGAAATTGAGCCCATGGATTTTTCTCCCAAATTTGAACATCTGGTATATAAAATGGATGAGACCCAATTCCCAACCACA
AAATCTGACATTATGCAAGAGGACACTGTACACCAATTGGAGTTTCAAGAGACTGATAATTATACTCTGAAGCAAAGTTC
TTATGTGGGCTGGTGGGTCCATAAGTTCCTTGTTGAAATGGCAGTGATTGTGGACCATACTCTCTACCTTCATTATGAAA
AGAACGTCTCAAAGTTGCAGGATGATCTATATGTTATTGTAAATATAGTGGATTCCATTTATGAGGTAATGGGTATTAAG
TTGTTATTACTTGGTATGGAGGTCTGGACTGAAAAAAACTACTTTGAAGTAGGTGATATAAGCAGATCTCTGAAGCAATT
TTGTGAGTGGAAGTCCAAAAATTTTGCTCCCCGCGTGTCACATGATACTGCACATCTTTTTACATATAAGACATTAAGAG
GATTAACTGGTTTAGGCTTCGTTGCAGGGCTGTGTAAATCACACAGAAATTGTGCAGTTGTTACTTGTGTTAACAAAACC
TTGTCCATTATTGGAATTGCAATGGCTCATCATCTAGGTCATAATTTGGGGATGTTTCATGATGCTGACGAGTGTAAGTG
TGCACATCCTACATGTATAATGCGCTATGATAACCCACCAATAACTCAATTTAGCAATTGTAGTTATAATTTCTTTTGGG
AATATTCTATACGCCAGGCAAAATGTTTGATGTACACTGTGCATACAAAGGATGTGTTTACAATGAAGCGCTGTGGGAAT
GGCATTGTTGAAGAAGAAGAGGAGTGTGACTGTGGAATTTTAAGGAGTTGTTCAAAAGATCCCTGTTGTCTGTCAAACTG
CACTCTGAGTTTTGGATCTATTTGTGCTTTTGGGCTTTGTTGCAAGGACTGCGAGTTTTTACCATCAGGGAGAGTATGTA
GAAAGAAAGTCAATGAATGTGATCTTCCAGAGTGGTGCAATGGAACATCCCATATGTGTCCAGATGATGTATATGTGGAG
GACGGAATTCCTTGTAATAGCAGTGCCTACTGCTATGAAAAAAGCTGTCATAACCGTGATGAACAGTGTAGGCAGATCTT
TGGCCAAGAGGCAAAGAGTGCAAATAACAGTTGTTACAAACGAGTAAACACTAAAGGTGACCGTTTTGGTAACTGTGGTT
TCAAAGACTTTTCATATGTAAAATGTGATAGCTCAGATAGCCTGTGTGGGAGGGTTCAGTGTGAGAATGTGACAAAAATT
CCCCTTTTGAGTGATCATTCTACTGTGCATTGGACTCGCGTCAATGGTGCCATCTGCTGGGGTATAGACTACCATTTTGG
GATGACTACACCTGATATTGGTGATGTGAAAGATGGCACAGAGTGTGGCCCAGAACACGTCTGCATCCACAGGAAGTGTG
TCCATTTATCTCGCTTGGATAGTAATTGTTCACCTAAGTTTTGTAACATGAGGGGGATCTGTAACAATAAACATCACTGC
CATTGCAACTATATGTGGGACCCTCCCAATTGCCTAATAAGAGGCAGTGGAGGTAGTATCGACAGTGGCCCACCCCCTAA
GAGAGAGAAGATTAAGAAGATTTACGTGTTAGGATTTGTGCTTTTTTGGTTGATTGTTTTATTATGTTGTCTTCTTTTGC
TTTGTAAGAAGAAAAAATCTAAGAAAAAAGACCAAAAAGTTCAGGCTGAAGTTAAAAAAGCAGAAAATGTCAAGACACAA
CAACCAAAAGAA
ORF - retro_ecab_25 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.82 % |
| Parental protein coverage: | 99.25 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VRLILLLLWLRVFLFLSALSQVGLSSHHGPPEVVIPLRFARSAAGSPVFRWLSYRMNFGGQRHIVHMKVN |
| .R..LL..WL.VFL..S..........H.PPEVVIPL...R...G......LSY...FGG.RH.VH..V. | |
| Retrocopy | MRITLLIHWLAVFLSSSGHMWPENPQYHSPPEVVIPLKLPRTGRGMKPPGMLSYSLHFGGKRHVVHLRVK |
| Parental | KHFLYRHLSVFTYTDQGTLLEDQPFVQNDCYYHGYVE-DSESLVSLNTCVGGFQGIIQTMDTIYEITPKR |
| KH.L.RHL.VFTYTDQG.LLE..PFVQNDCYYHGYVE.D.ESLV.L.TC.GGFQG..Q.....YEI.P.. | |
| Retrocopy | KHLLSRHLPVFTYTDQGALLEEKPFVQNDCYYHGYVEGDLESLVALSTCSGGFQGLLQINSIVYEIEPMD |
| Parental | LTI-FEHLVHRIDSEETQSPPMRCGLTDEEIARQLKLQGSDTFTLMRTPYEGWWLHKRYLEIAVVVDNNR |
| ....FEHLV...D..ETQ.P........E....QL..Q..D..TL....Y.GWW.HK...E.AV.VD... | |
| Retrocopy | FSPKFEHLVYKMD--ETQFPTTKSDIMQEDTVHQLEFQETDNYTLKQSSYVGWWVHKFLVEMAVIVDHTL |
| Parental | FIHRDSNVSDVQKEAYEVIHHTNNFFKTVDIEVTLMGIEIWTEGNLILLDDIYRGLRRFCDWKRQGFNDR |
| ..H...NVS..Q...Y..............I...L.G.E.WTE.N.....DI.R.L..FC.WK...F..R | |
| Retrocopy | YLHYEKNVSKLQDDLYVIVNIVDSIYEVMGIKLLLLGMEVWTEKNYFEVGDISRSLKQFCEWKSKNFAPR |
| Parental | LPHDAAHIFSGKGFGIVGGLAYVGTVCNSRHNCGIESFQTEDLVSFANTVTHEVGHTVGMKHDDGTCTCG |
| ..HD.AH.F..K......GL..V...C.S..NC.........L........H..GH..GM.HD...C.C. | |
| Retrocopy | VSHDTAHLFTYKTLRGLTGLGFVAGLCKSHRNCAVVTCVNKTLSIIGIAMAHHLGHNLGMFHDADECKCA |
| Parental | RSRCIMNAGKGDTHRFSNCSYTWYSELMLR-TKCMYIPPSPERIFTMTRCGNSVVEEGEECDCGSL-TCI |
| ...CIM.........FSNCSY....E...R..KC..........FTM.RCGN..VEE.EECDCG.L..C. | |
| Retrocopy | HPTCIMRYDNPPITQFSNCSYNFFWEYSIRQAKCLMYTVHTKDVFTMKRCGNGIVEEEEECDCGILRSCS |
| Parental | EDHCCQSNCTLIPEADCAFGLCCQDCKFMPSGTMCRKKENECDLPEWCNGTSHQCPEDVYMQDGFLCKSG |
| .D.CC.SNCTL.....CAFGLCC.DC.F.PSG..CRKK.NECDLPEWCNGTSH.CP.DVY..DG..C.S. | |
| Retrocopy | KDPCCLSNCTLSFGSICAFGLCCKDCEFLPSGRVCRKKVNECDLPEWCNGTSHMCPDDVYVEDGIPCNSS |
| Parental | DYCYEKRCNNRDEQCRKIFGKEAKSANQSCYMRINTRGDRFGHCGLKNTAFVRCNTSDSLCGRVQCENVT |
| .YCYEK.C.NRDEQCR.IFG.EAKSAN.SCY.R.NT.GDRFG.CG.K....V.C..SDSLCGRVQCENVT | |
| Retrocopy | AYCYEKSCHNRDEQCRQIFGQEAKSANNSCYKRVNTKGDRFGNCGFKDFSYVKCDSSDSLCGRVQCENVT |
| Parental | KIPFLEEHSTVHWTHFNDVTCWGTDYHYGMTIPDIGEVKDGTECGVDHICIQKKCMPMSHLDRDCSPETC |
| KIP.L..HSTVHWT..N...CWG.DYH.GMT.PDIG.VKDGTECG..H.CI..KC...S.LD..CSP..C | |
| Retrocopy | KIPLLSDHSTVHWTRVNGAICWGIDYHFGMTTPDIGDVKDGTECGPEHVCIHRKCVHLSRLDSNCSPKFC |
| Parental | NMKGVCNNRHH-HCNYPWDPPDCLKNGTGGSIDSGPP |
| NM.G.CNN.HH.HCNY.WDPP.CL..G.GGSIDSGPP | |
| Retrocopy | NMRGICNNKHHCHCNYMWDPPNCLIRGSGGSIDSGPP |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP021940_articular_cartilage | 0 .00 RPM | 0 .00 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP021940_embryo | 0 .03 RPM | 0 .00 RPM |
| SRP021940_placental_villous | 0 .05 RPM | 0 .00 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 0 .00 RPM |
| SRP021940_testis | 64 .52 RPM | 39 .33 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_25 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_25 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_25 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000023845 | 1 retrocopy |
retro_ecab_25 ,
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