RetrogeneDB ID: | retro_ecab_6 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 2:71046665..71048546(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000002749 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TKTL1 | ||
| Ensembl ID: | ENSECAG00000021992 | ||
| Aliases: | None | ||
| Description: | transketolase-like 1 [Source:HGNC Symbol;Acc:11835] |
Retrocopy-Parental alignment summary:
>retro_ecab_6
ACCATAGCCGACAACGCCAAGCCCCGTGCGAATACGTTGCAGGTGCTGCGGGACATGGCCAACCGCCTGCGGATCCATTC
CATCAGGGCCACGTGTGCCTCCCGCTCCGGCCACCCCACGTCGTGCTGCAGCGCAGCTGAGATCATGTCCGTGCTGTTCT
TCCACACGATGCGGTATAAACAGACAGAGCCGGAACACCCTGACAACGACCGATTCATCCTCTCCAAGGGCCATGCTGCT
CCCATCCTCTATGCGGCTTGGGCAGAGCTGGGCATCATCAGTGAATCCGACTTGCTGAACTTGAGGAAAATTAACTGTGA
CTTAGAGGGACATCCCACCCCAAGACTGTCGTTCGTTGATGTGGCAACCGGATCGCTTGGGCAAGGATTGGGTGCCGCCT
GCGGAATGGCTTATACTGGCAAGTACTTTGACAAGGCCAGCTACCGAGTGTTCTGCCTTATGGGAGATGGTGAATCCTCG
GAAGGTTCAGTCTGGGAGGCTCTGGACTTCGCTTCCCACTACAATTTGGACAATCTCGTGGCAGTCTTTGACGTGAACCG
TTTGGGACAAAGTGGTGTCACGCCCCTTGAGCACTGCACAGACGTCTATCAGAATCGCTGTGAAGCCTTTGGGTGGAATA
CTTACTTAGTGGATGGCCATGATGTGGAGGGGTTGTGCCATGCGTTCTGGCAAGCAACTCAAGTGAAGAACAAGCCCACT
GCCATAGTAGCCAAGACCTTCAAGGGCCGGGGTATTCCAGACATTGAGGATGCAGAAAATTGGCATGGAAAGCCAATGCC
AAAAGAAAGAGCAGATGCAATCATCAAATTAATTGAGAGTCAGATACAGACCAATAGAAATTTCATAGTGAAACCCCCTC
TTGAAGACTCACCGCAAGTCAGCATCAGGAATATAAAAATGACCTGTCTGCCTGATTATGAAGTTGGTGACAAGATAGCT
ACTCAGAAAGCATATGGTTTGGCTCTGGTTAAACTGGGACGTGCAAATGACAGACTTATTGTGCTGGATGGTGACGCAAA
GAACTCCACCTTTTCTGAGATATTCAAGAAAGAATACCCTGAGCGTTTCATTGAGTGTGTTATGGCTGAGCAAAACATGG
TAAGTGTGGCACTGGGCTGCGCCACACGTGATCGAACTGTTGCTTTTATTAGTACCCTTGCTGCCTGTTTGACCCGAGCA
TTTGATCAGATCCGGATGGGAGCCATATCTCAAACCAATATCAATCTTATTGGTTCCCACTGCGGGGTATCTATGGGTGA
AGAAGGATCCTCCCAGATGGCTCTGGAGGATCTCGCCATGTTCCGAAGCATTCCCAATTGCACCGTTTTCTATCCAAGTG
ATGCCATCTCGGCAGAGCATGCTGTTTATCTGGCTGCCAGTACCAAAGGAATGTGCTTCATTCGGACCAGCCGACAAGAA
ACTGCCGTTATTTATACCCCACAAGAAAATTTTGTGATTGGACAGGCCAGGGTCATCCGCCACAGTGTCAATGACAAAGT
TACAGTTATTGGAGCAGGAGTTACTCTCCATGAAGCCTTAGCAGCTGCTGCTGATCTTTCTCAACAAGGCATTTCTATCC
GTGTCATTGACCCGTTTACCATTAAACCCCTGGATGCTGCCACCATCATCTCCAGTGCAAAAGCTACAGGTGGTCGGGTT
ATCACAGTAGAGGATCACTACCGAGAAGGTGGCCTTGGAGAAGCTGTGTGTACAGCTGTCTCTGGGGAGCCTGACATCCT
TGTTCATCAGCTGGCAGTGTCAGGAGTGCCCCAAAGTGGGAAACCTGGTGAATTGCTGGATATGTTTGGAATCAGTGCCA
GACACATCATAGCTGCTGTGAAATACACTTTAATGAACTAA
ORF - retro_ecab_6 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.03 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEETKPDAKTVQVLQDMANRLRIQSIRAACASSSGHPTSCSSAAEIMAVLFFHTMRYKQADPDDPDNDR |
| .A...KP.A.T.QVL.DMANRLRI.SIRA.CAS.SGHPTSC.SAAEIM.VLFFHTMRYKQ..P..PDNDR | |
| Retrocopy | IADNAKPRANTLQVLRDMANRLRIHSIRATCASRSGHPTSCCSAAEIMSVLFFHTMRYKQTEPEHPDNDR |
| Parental | FVLSKRGWPLRALRCRWTQQATISRSDLLGSRKIGFDLEGHPTPRLSFVDVATGWLGQGLGAACGMAYTG |
| F.LSK.G.....L...W.....IS.SDLL..RKI..DLEGHPTPRLSFVDVATG.LGQGLGAACGMAYTG | |
| Retrocopy | FILSK-GHAAPILYAAWAELGIISESDLLNLRKINCDLEGHPTPRLSFVDVATGSLGQGLGAACGMAYTG |
| Parental | KYFDKASYRVFCLLGDGEFSEGSVWEALAFASHYSLDNLVAVFDVNRLGHSGTLPLENCIDVYQKRCEAF |
| KYFDKASYRVFCL.GDGE.SEGSVWEAL.FASHY.LDNLVAVFDVNRLG.SG..PLE.C.DVYQ.RCEAF | |
| Retrocopy | KYFDKASYRVFCLMGDGESSEGSVWEALDFASHYNLDNLVAVFDVNRLGQSGVTPLEHCTDVYQNRCEAF |
| Parental | GWNTYVVDGRDVEALCQVFWQAAQVKNKPTAVVAKTFKGRGIPNVEDAENWHGKPMPKERADAIIKLIES |
| GWNTY.VDG.DVE.LC..FWQA.QVKNKPTA.VAKTFKGRGIP..EDAENWHGKPMPKERADAIIKLIES | |
| Retrocopy | GWNTYLVDGHDVEGLCHAFWQATQVKNKPTAIVAKTFKGRGIPDIEDAENWHGKPMPKERADAIIKLIES |
| Parental | QIETNQNLEPKPPIEDSPQITITDIEMTSPPAYKDGDKIATRKACGLALAKLGHANNRVIVLDGDTKNST |
| QI.TN.N...KPP.EDSPQ..I..I.MT..P.Y..GDKIAT.KA.GLAL.KLG.AN.R.IVLDGD.KNST | |
| Retrocopy | QIQTNRNFIVKPPLEDSPQVSIRNIKMTCLPDYEVGDKIATQKAYGLALVKLGRANDRLIVLDGDAKNST |
| Parental | FSEIFKKEHPERFIECFIAEQNMVSVALGCAIRDRTIAFVSTFAAFLTRAFDQIRVGAISQSNINLIGSH |
| FSEIFKKE.PERFIEC..AEQNMVSVALGCA.RDRT.AF.ST.AA.LTRAFDQIR.GAISQ.NINLIGSH | |
| Retrocopy | FSEIFKKEYPERFIECVMAEQNMVSVALGCATRDRTVAFISTLAACLTRAFDQIRMGAISQTNINLIGSH |
| Parental | CGVSVGEDGPSQMALEDLAMFRAVPNCTIFYPSDAISTEHAVFLAANTKGMCYIRTSRPETSVIYTAQER |
| CGVS.GE.G.SQMALEDLAMFR..PNCT.FYPSDAIS.EHAV.LAA.TKGMC.IRTSR.ET.VIYT.QE. | |
| Retrocopy | CGVSMGEEGSSQMALEDLAMFRSIPNCTVFYPSDAISAEHAVYLAASTKGMCFIRTSRQETAVIYTPQEN |
| Parental | FEIGQAKVVRHSVNDKVTVIGAGVTLHEALAAADDLSKQDISVRVIDLFTIKPLDAATIISNAKATGGRI |
| F.IGQA.V.RHSVNDKVTVIGAGVTLHEALAAA.DLS.Q.IS.RVID.FTIKPLDAATIIS.AKATGGR. | |
| Retrocopy | FVIGQARVIRHSVNDKVTVIGAGVTLHEALAAAADLSQQGISIRVIDPFTIKPLDAATIISSAKATGGRV |
| Parental | ITVEDHYPEGGIGEAVCAAVSMEPDILVHQLAAPGVPQSGKPSELLDMFGVSARHIIVAVKCMLMN |
| ITVEDHY.EGG.GEAVC.AVS.EPDILVHQLA..GVPQSGKP.ELLDMFG.SARHII.AVK..LMN | |
| Retrocopy | ITVEDHYREGGLGEAVCTAVSGEPDILVHQLAVSGVPQSGKPGELLDMFGISARHIIAAVKYTLMN |
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 .05 RPM | 0 .68 RPM |
| SRP021940_embryo | 0 .00 RPM | 0 .03 RPM |
| SRP021940_placental_villous | 0 .05 RPM | 0 .19 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 0 .00 RPM |
| SRP021940_testis | 129 .55 RPM | 206 .60 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_6 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_6 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_6 has 6 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_47 |
| Pan troglodytes | retro_ptro_126 |
| Macaca mulatta | retro_mmul_74 |
| Mus musculus | retro_mmus_220 |
| Oryctolagus cuniculus | retro_ocun_62 |
| Bos taurus | retro_btau_176 |
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000018441 | 1 retrocopy | |
| Equus caballus | ENSECAG00000021992 | 1 retrocopy |
retro_ecab_6 ,
|
| Felis catus | ENSFCAG00000011392 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000005145 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000020870 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000005014 | 1 retrocopy |