RetrogeneDB ID: | retro_ecab_840 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 5:63521740..63522157(+) | ||
| Located in intron of: | ENSECAG00000021205 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SOD2 | ||
| Ensembl ID: | ENSECAG00000011797 | ||
| Aliases: | SOD2, Mn-SOD | ||
| Description: | superoxide dismutase [Source:RefSeq peptide;Acc:NP_001075986] |
Retrocopy-Parental alignment summary:
>retro_ecab_840
AGGCTTCTATACAGCCTCCCTGTCTTATCTTATGATTATGGTGCTCTGGGGCCTAACATTAATGCACAAAGCAGGCAGCT
GCACCACCGTCAACATCATGTCAATTGTGTGAATAACTTGACTCCTGCCAAGGAGAAATATAAAGGGCCCCTGGCAAAAT
ATGATGTTATAATTCAGGTAGCTCTTCAGCCTGCACTTAAGTTCAGTGGTGGAGGCCGTGCCACTCTTACCATTTTATGG
ACAAACCTAAGCCCTGTAGATGGTGGAGAGCCCAAACTGGAGTTGCTGGAAGCCAGCGAATGTTACTTTGTTTCCTTTGG
TTAACTTAAGGAGAAGTTGACAGCTGTATCTGTTGGCATTCAAGGTTCAGACTGGGATTGGCTTGCTTTCATTAAGTAAC
ACAGATTGCAGCTTGTT
ORF - retro_ecab_840 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.14 % |
| Parental protein coverage: | 64.22 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RQKHSLPDLQYDYGALEPYINAQIMQLHHSKHHAAYVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNG |
| R...SLP.L.YDYGAL.P.INAQ..QLHH..HH...VNNL....EKY...LAK.DV..Q.ALQPALKF.G | |
| Retrocopy | RLLYSLPVLSYDYGALGPNINAQSRQLHHRQHHVNCVNNLTPAKEKYKGPLAKYDVIIQVALQPALKFSG |
| Parental | GGHINHTIFWTNLSPNGGGEPKGELLDAIKRDFGSFDKFKEKLTAVSAGVQGSGWGWLGFNKDQGRLQIV |
| GG....TI.WTNLSP..GGEPK.ELL.A....F.SF...KEKLTAVS.G.QGS.W.WL.F.K...RLQ.V | |
| Retrocopy | GGRATLTILWTNLSPVDGGEPKLELLEASECYFVSFG*LKEKLTAVSVGIQGSDWDWLAFIK*H-RLQLV |
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 | 63 .69 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 34 .90 RPM |
| SRP021940_embryo | 0 .00 RPM | 13 .94 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 53 .60 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 112 .77 RPM |
| SRP021940_testis | 0 .00 RPM | 12 .53 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_840 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_840 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_840 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Canis familiaris | retro_cfam_1795 |
| Callithrix jacchus | retro_cjac_3032 |