RetrogeneDB ID: | retro_ecab_780 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 4:28300981..28301410(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SGTA | ||
| Ensembl ID: | ENSECAG00000010381 | ||
| Aliases: | None | ||
| Description: | small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha [Source:HGNC Symbol;Acc:10819] |
Retrocopy-Parental alignment summary:
>retro_ecab_780
GGCCTGCGCGGTCTATGTCTGTACCAGAGCTTCCGCACAAGCACACTGAACTACTACTACGAGGAGGCCTTGGAGCTGGG
CCCGGACTAGAAGACTTGCAAGTCGAATCTCAAGATAGCCAACTGAAGCTGAGAGAGGGCCAAGTCCCACAGGAAGCTTT
GACATCACCGGCAAGCTGAAGAACCCAAGCTTCAGGAGCATGGCGTCAAACCTAATGAACAATCCCCAAGTTCAACAGCT
CATGTCTGGGATGATTTCGGTGGCCATAAACACTTAGGGACTCCTGGCACCAACCCTTCACAGAAAGACCTGGCCAATCT
CATCCAGGCGGGCCAGGAGTTCGTTCAGCAGATGCAGCAGCAAAATCCAGAGTTGACAGAACAGCTCAGAAGTCAGACCC
CCAGGGCCAACAAGGATGACCTGCAGGAA
ORF - retro_ecab_780 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.53 % |
| Parental protein coverage: | 69.91 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | GRMGLALSSLNKHTEAVAYYKKALELDPDNEKYKSNLKIA-ELKLQEGT-SPTGGVGSFDIAGLLNNPSF |
| G..GL.L...........YY..ALEL.PD....KSNLKIA..LKL.EG..SPT...GSFDI.G.L.NPSF | |
| Retrocopy | GLRGLCLYQSFRTSTLNYYYEEALELGPD*KTCKSNLKIA<QLKLREGQ<SPT---GSFDITGKLKNPSF |
| Parental | MSMASNLMNNPQVQQLMSGMIS-GGHNPLGTPGTSPSQNDLASLIQAGQQFAQQMQQQNPELIEQLRSQI |
| .SMASNLMNNPQVQQLMSGMIS.GGH..LGTPGT.PSQ.DLA.LIQAGQ.F.QQMQQQNPEL.EQLRSQ. | |
| Retrocopy | RSMASNLMNNPQVQQLMSGMIS<GGHKHLGTPGTNPSQKDLANLIQAGQEFVQQMQQQNPELTEQLRSQ- |
| Parental | RSRTPSASNDDQQE |
| ...TP.A..DD.QE | |
| Retrocopy | ---TPRANKDDLQE |
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 | 14 .17 RPM |
| SRP021940_cerebellum | 0 .05 RPM | 31 .63 RPM |
| SRP021940_embryo | 0 .00 RPM | 40 .89 RPM |
| SRP021940_placental_villous | 0 .05 RPM | 15 .06 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 16 .39 RPM |
| SRP021940_testis | 0 .00 RPM | 53 .65 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_780 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_780 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_780 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 | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000005257 | 1 retrocopy | |
| Equus caballus | ENSECAG00000010381 | 2 retrocopies |
retro_ecab_723, retro_ecab_780 ,
|
| Monodelphis domestica | ENSMODG00000004900 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000004937 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000011900 | 1 retrocopy |