RetrogeneDB ID: | retro_ecab_726 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 3:75220458..75221167(+) | ||
| 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_726
GTACACCAGGATTTCATTTTCAAGATGGACAGCCCATCAGACTCAGCTATGGTTTCACGTCGCACACCACAGGCTTGTGC
CAGGTCACCGTCTCCCCATACCAGTAGTTCAAGAAAACAACCTATGAGTGCAACACTTAGAGAACGATTAAGGAAAACCA
GATCTTCATTTAATTCCTGTTACAGTATGGTAAAACGTCTCAAAGTAGAGAATGAAGATGATCAGAACCTTTCAGAGAAA
CCAGCAACTTCAGTAGAAGAAAACCGTGTGGAATTTCGAGAAGATTTTAAACACAGACAGTGAATTTGAAGAAAATACGT
ATTTGAAAAATACCTTCGAGAATATCAATGCATGTGAATCTGATTCACTCGATGCTGGGTCATGCAGTGAGGATCTCCAA
AATGACTTTGTGAATGAGAATCTTCCCCAAAAAGGATTAAATGAAGAAAAAGCAAAATTGGTGAAGCAGATTCAGGAGAA
AGAGGACCTTCTTCAGAGGCTGAAACTAGTCAAAATGTACAGATCAAAGAATGACCTATCTCAGTTACATTGTTAATAAA
GAAGTGGAGAAGCTGTAGCCAGCTGTTGCTTTACGAGTTACAGTCAGCTGTCCGAGGAAAACAAGAAACTCAGCCTTACT
CAGTTGATAGACTACTATGGCTTAGATGATAAATTGCTACCCTATAACAGAAATGAAGAAGAATTTATA
ORF - retro_ecab_726 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.27 % |
| Parental protein coverage: | 97.95 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | VNQDFIFKMESPSDSAVISPGTPQACARPPSPHTSSSRKQPMSATLRERLRKTRSSFNSCYSVVKRLKVE |
| V.QDFIFKM.SPSDSA..S..TPQACAR.PSPHTSSSRKQPMSATLRERLRKTRSSFNSCYS.VKRLKV. | |
| Retrocopy | VHQDFIFKMDSPSDSAMVSRRTPQACARSPSPHTSSSRKQPMSATLRERLRKTRSSFNSCYSMVKRLKV- |
| Parental | NEGDDQNFSEKPPTSVEENS-VEFREDVKRIDSEFEENTSLKNTFKDISACESESLHAGSCSEDLQNDFV |
| .E..D.......P....E...V...E.....DSEFEENT.LKNTF..I.ACES.SL.AGSCSEDLQNDFV | |
| Retrocopy | -ENEDDQNLSEKPATSVEEN>VWNFEKILNTDSEFEENTYLKNTFENINACESDSLDAGSCSEDLQNDFV |
| Parental | NEDLPREGLNEEKAKLVKQIQEKEDLLRRLKLVKMYRSKNDLSQLQ-LLIKRWRSCSQLLLCELQSAL-S |
| NE.LP..GLNEEKAKLVKQIQEKEDLL.RLKLVKMYRSKNDLSQL..LLIK.WRSCSQLLL.ELQSA... | |
| Retrocopy | NENLPQKGLNEEKAKLVKQIQEKEDLLQRLKLVKMYRSKNDLSQLH<LLIKKWRSCSQLLLYELQSAV>E |
| Parental | EENKKLSLTQLIDYYGLDDKLLHYNRNEEEFI |
| E..K.LSLTQLIDYYGLDDKLL.YNRNEEEFI | |
| Retrocopy | ENKK-LSLTQLIDYYGLDDKLLPYNRNEEEFI |
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 .00 RPM | 2 .05 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 1 .92 RPM |
| SRP021940_synovial_membrane | 0 .00 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_726 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_726 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_726 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 |