RetrogeneDB ID: | retro_ecab_121 | ||
Retrocopylocation | Organism: | Horse (Equus caballus) | |
| Coordinates: | 1:34505219..34505797(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | SMARCB1 | ||
| Ensembl ID: | ENSECAG00000007797 | ||
| Aliases: | None | ||
| Description: | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 [Source:HGNC Symbol;Acc:11103] |
Retrocopy-Parental alignment summary:
>retro_ecab_121
AAGAAAACAGTTGTATCCTCACATGGTCATGGATACATGATCCTGGCCACTAGTGTGACTCAGTTAAAAGCCTCAGTGGT
GGAAGAGATTCTGGAGGACAATGATGAGAAACACAAGGCATGTGTCCATCAGCATAGGGTTCCCCATCCATTTCAGGGAA
TGAGAAATCAAGAGGAATAGCCAGTGGGTGCCCACCCTGCTCAGCAGCTCTCACCATCTGCACACCGTGCCATGCTCCAC
AGCCATTAATAGGAACCTCATGGGCTAAGATAAGAAAGGAAGCTTCCCTCTCTGCTTTGATGATCATGACCCACCTGTGA
TCCATGAGAACACATCCCAGTCTAAAGTTTTGGTTCCCATCCGGCTGGACACGGAGATAGATGGGTAGAAGTGGAGGATG
CCTTTACATGAAACATGAATAAGAAGCTGATGACCTCTGAGATGTTTTCAGAAATCCTCTGTGACCACTTGGATTTGAAC
CCACTCATATTCATTCCTGCTTTCACCTCCATCATCAGACAGCAGATGGAGTCCTACCCACTGACAGCATCTTGGAGGAC
CAGTCCGACCAACGTGTC
AAGAAAACAGTTGTATCCTCACATGGTCATGGATACATGATCCTGGCCACTAGTGTGACTCAGTTAAAAGCCTCAGTGGT
GGAAGAGATTCTGGAGGACAATGATGAGAAACACAAGGCATGTGTCCATCAGCATAGGGTTCCCCATCCATTTCAGGGAA
TGAGAAATCAAGAGGAATAGCCAGTGGGTGCCCACCCTGCTCAGCAGCTCTCACCATCTGCACACCGTGCCATGCTCCAC
AGCCATTAATAGGAACCTCATGGGCTAAGATAAGAAAGGAAGCTTCCCTCTCTGCTTTGATGATCATGACCCACCTGTGA
TCCATGAGAACACATCCCAGTCTAAAGTTTTGGTTCCCATCCGGCTGGACACGGAGATAGATGGGTAGAAGTGGAGGATG
CCTTTACATGAAACATGAATAAGAAGCTGATGACCTCTGAGATGTTTTCAGAAATCCTCTGTGACCACTTGGATTTGAAC
CCACTCATATTCATTCCTGCTTTCACCTCCATCATCAGACAGCAGATGGAGTCCTACCCACTGACAGCATCTTGGAGGAC
CAGTCCGACCAACGTGTC
ORF - retro_ecab_121 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.39 % |
| Parental protein coverage: | 53.02 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | KKTKPNTKDHGYTTLATSVTLLKASEVEEILDGNDEKYKA-VSISTEPPTYLREQKAKRNSQWVPTLPNS |
| KKT......HGY..LATSVT.LKAS.VEEIL..NDEK.KA.VSIS...P...RE...KRNSQWVPTL..S | |
| Retrocopy | KKTVVSSHGHGYMILATSVTQLKASVVEEILEDNDEKHKA>VSISIGFPIHFRE*EIKRNSQWVPTLLSS |
| Parental | SHHLDAVPCSTTINRNRMGRDKKRTFPLCFDDHDPAVIHENASQPEVLVPIRLDMEIDGQKLR-DAFTWN |
| SHHL..VPCST.INRN.MG.DKK..FPLCFDDHDP.VIHEN.SQ..VLVPIRLD.EIDG.K.R.DAFT.N | |
| Retrocopy | SHHLHTVPCSTAINRNLMG*DKKGSFPLCFDDHDPPVIHENTSQSKVLVPIRLDTEIDG*KWR<DAFT*N |
| Parental | MNEKLMTPEMFSEILCDDLDLNPLTFVPAIASAIRQQIESYHL-DAVSRDKGQKRV |
| MN.KLMT.EMFSEILCD.LDLNPL.F.PA..S.IRQQ.ESY.L.D....D....RV | |
| Retrocopy | MNKKLMTSEMFSEILCDHLDLNPLIFIPAFTSIIRQQMESYPL<DSILEDQSDQRV |
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 | 20 .01 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 81 .69 RPM |
| SRP021940_embryo | 0 .03 RPM | 147 .20 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 43 .44 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 48 .43 RPM |
| SRP021940_testis | 0 .00 RPM | 57 .93 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_121 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_121 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_121 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000007797 | 2 retrocopies |
retro_ecab_120, retro_ecab_121 ,
|