RetrogeneDB ID: | retro_ecab_639 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 24:28121650..28122352(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CSK | ||
| Ensembl ID: | ENSECAG00000013581 | ||
| Aliases: | None | ||
| Description: | c-src tyrosine kinase [Source:HGNC Symbol;Acc:2444] |
Retrocopy-Parental alignment summary:
>retro_ecab_639
CCCAAGACAGGCCTGTTCCTGGTGTGGGAGAGCATCAACTACCCTGGGGACTATACGCTGTCTGTGAACTGTGAAGGCAA
AGTGGAGCACTACAGCATCATGTACGACAACAGCAAGCTCAGCATTAGTGAGGAGGTGTACTTCGAGAGCCTCATGCAGC
TGGTGGAGCACTACACCTCAGGTGCAGATGAAATCTGTACTTGCCTCATCAAGCCAAAGGTCATGGAGGGCACAGAGGAG
GTCCAGGATGAGCTCTTCCTCAGAGGCTGGACGCTGAACATAAAGGACCTGAAGCTGCTGCAGATCACTGGGAAGGGGGA
CTTTGGAGACGTGATGCTGAGCTGTTGTGGAGGGAACAAAGTCTCTGTCAATTACGTTAGGAACGACACTACTGCCCAAG
CATTCCTGGCTGAAGCCTTGGTCATGGCACAAGTTCATCCTAGCAACCAGGTACAGCTTTTGGGCGTGATCACGGCGCAG
AAACGTGGCCTTTACATCATCACTGAGTTCATGGCCAAGGGGAGCCTGGTGGATTACCGGCAGTTGCTGGATTGGTAGGT
GCTGGGCAGAGACTTTCTCCTCAAATTCTCACTAGACCTCCGTGAGACCATGAAGTACCCAGAGAGCAACAACTTCGTAC
ACCGGGGCCTTGCTGCCGGCGCCATGCTGGTATCCGAGGACAGCGTGGCCAAGGTCAAGGAC
ORF - retro_ecab_639 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.51 % |
| Parental protein coverage: | 52.12 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PETGLFLVRESTNYPGDYTLCVSCDGKVEHYRIMYHASKLSIDEEVYFENLMQLVEHYTSDADGLCTRLI |
| P.TGLFLV.ES.NYPGDYTL.V.C.GKVEHY.IMY..SKLSI.EEVYFE.LMQLVEHYTS.AD..CT.LI | |
| Retrocopy | PKTGLFLVWESINYPGDYTLSVNCEGKVEHYSIMYDNSKLSISEEVYFESLMQLVEHYTSGADEICTCLI |
| Parental | KPKVMEGTVAAQDEFFRSGWALNMKDLKLLQTIGKGEFGDVMLGDYRGNKVAVKCIKNDATAQAFLAEAS |
| KPKVMEGT...QDE.F..GW.LN.KDLKLLQ..GKG.FGDVML....GNKV.V....ND.TAQAFLAEA. | |
| Retrocopy | KPKVMEGTEEVQDELFLRGWTLNIKDLKLLQITGKGDFGDVMLSCCGGNKVSVNYVRNDTTAQAFLAEAL |
| Parental | VMTQLRHSNLVQLLGVIVEEKGGLYIVTEYMAKGSLVDYLRSRGRSVLGGDCLLKFSLDVCEAMEYLEGN |
| VM.Q...SN.VQLLGVI...K.GLYI.TE.MAKGSLVDY.......VLG.D.LLKFSLD..E.M.Y.E.N | |
| Retrocopy | VMAQVHPSNQVQLLGVITAQKRGLYIITEFMAKGSLVDYRQLLDW*VLGRDFLLKFSLDLRETMKYPESN |
| Parental | NFVHRDLAARNVLVSEDNVAKVSD |
| NFVHR.LAA...LVSED.VAKV.D | |
| Retrocopy | NFVHRGLAAGAMLVSEDSVAKVKD |
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 | 24 .67 RPM |
| SRP021940_cerebellum | 0 .05 RPM | 42 .48 RPM |
| SRP021940_embryo | 0 .00 RPM | 63 .96 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 30 .41 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 64 .46 RPM |
| SRP021940_testis | 0 .00 RPM | 25 .26 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_639 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_639 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_639 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000013581 | 1 retrocopy |
retro_ecab_639 ,
|
| Myotis lucifugus | ENSMLUG00000013625 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000001900 | 1 retrocopy |