RetrogeneDB ID: | retro_ecab_887 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 6:68560003..68560641(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SFR1 | ||
| Ensembl ID: | ENSECAG00000005386 | ||
| Aliases: | None | ||
| Description: | SWI5-dependent recombination repair 1 [Source:HGNC Symbol;Acc:29574] |
Retrocopy-Parental alignment summary:
>retro_ecab_887
ATGGCAGAGGGAGAGGTGAACCAAGATTTCATTTCCAAAATGGAAAATCCATCAGACTCAGCTGTGACCTTACCCAGCAT
TCCACAGGCCTGTGCCCATCCACCACCTCCCCACACAAACAGTTCAAGAAAACAACCCATGTGTGCAATACTTAGAGAAC
AATTGAGGAAAATAAGGTCTTCATTTAACTCCCGTGACAGCATGGTAAAATGTCTTAAAGTAGAGAGTGAAGAAAACATT
CAGACCTTTTCAGAGAAACCTGCACCTTCAACAGAAAACTGTTTGGAATTTCAAGAAAATTTCAAACACATAGACAGTGA
ATTTGAAGAAAGTACATATTGAAAAATACCTTCAAGAATATCAACACCTGTGAATCTAAAGCACTTGAACCTGGGTCACG
CAGTGATGATCTCCAAAATGATTTTGTGAATAAGAATCTTGCCAAACAAGGATGAAATGAAGGAAAAGCGAAATTGGTGA
AGCAGGTTCAGGAGAAAGAAGACTTTCTTCGGAGGCTAAAAGTAGTCAAAATGTGTAGATCAAAGAATGACCTGTCTCAG
GTACCGTTGTTAACACGGAAGTGGAGAAGCTGTTACGAGTCGCAGTGGGCTGTGTCTGAGCAGGACAAGAAACTGAGC
ORF - retro_ecab_887 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.44 % |
| Parental protein coverage: | 86.89 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEGEVNQDFIFKMESPSDSAVISPGTPQACARPPSPHTSSSRKQPMSATLRERLRKTRSSFNSCYSVVK |
| MAEGEVNQDFI.KME.PSDSAV..P..PQACA.PP.PHT.SSRKQPM.A.LRE.LRK.RSSFNS..S.VK | |
| Retrocopy | MAEGEVNQDFISKMENPSDSAVTLPSIPQACAHPPPPHTNSSRKQPMCAILREQLRKIRSSFNSRDSMVK |
| Parental | RLKVENEGDDQNFSEKPPTSVEENSVEFREDVKRIDSEFEENT-SLKNTFKDISACESESLHAGSCSEDL |
| .LKVE.E...Q.FSEKP..S..EN..EF.E..K.IDSEFEE.T..LKNTFK.I..CES..L..GS.S.DL | |
| Retrocopy | CLKVESEENIQTFSEKPAPST-ENCLEFQENFKHIDSEFEEST<ILKNTFKNINTCESKALEPGSRSDDL |
| Parental | QNDFVNEDLPREGLNEEKAKLVKQIQEKEDLLRRLKLVKMYRSKNDLSQLQLLIKRWRSC--SQLLLCEL |
| QNDFVN..L...G.NE.KAKLVKQ.QEKED.LRRLK.VKM.RSKNDLSQ..LL...WRSC..SQ....E. | |
| Retrocopy | QNDFVNKNLAKQG*NEGKAKLVKQVQEKEDFLRRLKVVKMCRSKNDLSQVPLLTRKWRSCYESQWAVSEQ |
| Parental | QSALS |
| ...LS | |
| Retrocopy | DKKLS |
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 | 1 .71 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 0 .21 RPM |
| SRP021940_embryo | 0 .10 RPM | 2 .05 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 1 .92 RPM |
| SRP021940_synovial_membrane | 0 .03 RPM | 1 .02 RPM |
| SRP021940_testis | 0 .00 RPM | 1 .47 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_887 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_887 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_887 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000005386 | 2 retrocopies |
retro_ecab_726, retro_ecab_887 ,
|
| Echinops telfairi | ENSETEG00000015444 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000025713 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000015327 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000004202 | 1 retrocopy |