RetrogeneDB ID: | retro_ecab_551 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 20:24191912..24192906(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C4orf27 | ||
| Ensembl ID: | ENSECAG00000013735 | ||
| Aliases: | None | ||
| Description: | chromosome 4 open reading frame 27 [Source:HGNC Symbol;Acc:26051] |
Retrocopy-Parental alignment summary:
>retro_ecab_551
GAAGCACAGCGGTGTGAAAACACGGTTGATGGTGAAGAAGAGTAAATCCTGTGAAGCTGATATCTCCAATGACTTCAAAA
AGAGTAGGAAACCATTATAAGCTTTCTCTGCTTGAAGATTTCTATTGCTTCTCAAAGTTCTGTGAAGAACTTGACCCTGA
GAAAACAGTTGATCCACTTTCCCAAAGCCTTGGACTTCGATTAATGGGTCCTTCTGATGATATCCTTGCTGGAAAACATA
AAATGAAGAAAAAAATAGCAAGTTTGAATTTTAGCCTTAACTGGAGATATCACTAGGATACTCCTGAATTCCAGACCATT
ATTATTAGAGATAATAAAATTCATCACCACATAGCATATTTCAGGGATTTTTCTAGTGAACTTCCTGGATATGTTGGTAT
AAATAAAGCAAAGAAAAAAGGTATAATTATTGAAAATGGGGATAATGTGTTTGCTTCAGTTAAATTATTTTTGATGAAGA
AACTTAAAGAAATAACAGATAAAAAGAAAACTAGTCTCTTGAAAAACACAGACGAAAAACTCACAGAAGCAGCTAGAGAA
CTGGGATGCTCACTGGAACCGAGAACCATGAAGATGAAACAGAGAGATAAGAAAGTTGTGACGAAGACCTTTCGTGGTGC
AGGCTTGATTATCCCAGTAGATAAAAATGATGTTGGGTACAGAGAGCTCCCTGAAACAGATGCCAACCTCAAGAGAATTT
GCAAGACAACTGTTGAGGCAGCAAGTGATGAGGAGAGACTAACAGCTTTTGCTCCCATTCAGGAGGTGATGATTTTTGTG
CATTTTGCTAATGATGAATGTGATTATGGCATGGGGCTTGAGGTGGGAATGGACCTCTTTTGCTATAGTTCGCACTATTT
TCGTAAAGTTGCTGGCCAGGTTTTACCTCTTGTATGTAATGTGTTGAAGAGGAATTTCTTGCAGAAATTATTCAAGATCA
TCTGGCAAACAGAAGGAAAGAGAACGTGGACCAA
ORF - retro_ecab_551 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.27 % |
| Parental protein coverage: | 95.66 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | EGPQCEKTVD-VKKSKSCEADVSSD-LRKE-VENHYKLSLPEDFYHFWKFCEELDPEKPADSLSASLGLR |
| E...CE.TVD.VKKSKSCEAD.S.D.L.KE.V.NHYKLSL.EDFY.F.KFCEELDPEK..D.LS.SLGLR | |
| Retrocopy | EAQRCENTVD>VKKSKSCEADISND<LQKE<VGNHYKLSLLEDFYCFSKFCEELDPEKTVDPLSQSLGLR |
| Parental | LVGPYD-LLAGKHKMKKKSASLNFNLHWRFYYDPPEFQTIIIGDDKTQFHMGYFRDSPDELPVYVGTNEA |
| L.GP.D..LAGKHKMKKK.ASLNF.L.WR...D.PEFQTIII.D.K...H..YFRD...ELP.YVG.N.A | |
| Retrocopy | LMGPSDDILAGKHKMKKKIASLNFSLNWRYH*DTPEFQTIIIRDNKIHHHIAYFRDFSSELPGYVGINKA |
| Parental | KKNCIIVQNGDNVFAAVKLFLMKKLKEVTDKKKTSLLKNIDEKLTAAARELGYSLEQRTMKMKQRDKKVV |
| KK..II..NGDNVFA.VKLFLMKKLKE.TDKKKTSLLKN.DEKLT.AARELG.SLE.RTMKMKQRDKKVV | |
| Retrocopy | KKKGIIIENGDNVFASVKLFLMKKLKEITDKKKTSLLKNTDEKLTEAARELGCSLEPRTMKMKQRDKKVV |
| Parental | TKTFHGAGLVVPVDKNDVGYRELPETDANLKRICKTIVEAASDEERLKAFAPIQEMMTFVQFANDECDYG |
| TKTF.GAGL..PVDKNDVGYRELPETDANLKRICKT.VEAASDEERL.AFAPIQE.M.FV.FANDECDYG | |
| Retrocopy | TKTFRGAGLIIPVDKNDVGYRELPETDANLKRICKTTVEAASDEERLTAFAPIQEVMIFVHFANDECDYG |
| Parental | MGLELGMDLFCYGSHYFHKVAGQLLPLAYNLLKRN-LFAEIIEDHLANRSKENIDQ |
| MGLE.GMDLFCY.SHYF.KVAGQ.LPL..N.LKRN...AEII.DHLANR.KEN.DQ | |
| Retrocopy | MGLEVGMDLFCYSSHYFRKVAGQVLPLVCNVLKRN<FLAEIIQDHLANRRKENVDQ |
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 | 5 .19 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 6 .39 RPM |
| SRP021940_embryo | 0 .00 RPM | 11 .97 RPM |
| SRP021940_placental_villous | 0 .05 RPM | 9 .43 RPM |
| SRP021940_synovial_membrane | 0 .03 RPM | 4 .72 RPM |
| SRP021940_testis | 0 .00 RPM | 3 .64 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_551 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_551 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_551 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000020132 | 1 retrocopy | |
| Equus caballus | ENSECAG00000013735 | 1 retrocopy |
retro_ecab_551 ,
|
| Gorilla gorilla | ENSGGOG00000003090 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000017052 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000001481 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000009751 | 1 retrocopy |