RetrogeneDB ID: | retro_ocun_1403 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 8:28478189..28478993(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SRPRB | ||
| Ensembl ID: | ENSOCUG00000007623 | ||
| Aliases: | None | ||
| Description: | signal recognition particle receptor, B subunit [Source:HGNC Symbol;Acc:24085] |
Retrocopy-Parental alignment summary:
>retro_ocun_1403
GCGGACTCCCGGCGGCTGGGGGATGGCGACGGTGCCGGGGGCGCTTTCCAGCCCTATCTAGACTCCTTGCGGCAGGAGCT
GCAGCAGAGGGACCCGACGGTGCTGTCAGTAGTGGTGGCGCTTCTCGCGGTGTTGCTGACGCTGGTGTTCTGGAAGCTCG
TCTGCAGCAGAAGGAGCAGCCAGAGAGCGGTGCTGCTGCTCGGCCTTTGCGACTCCGGAAAGACGTTGCTGTTCGTCAGG
TTGTTAACAGGCCATTACAGAGACACCCAGACGTCCATCACAGATAGCTCTGCCACATACAGAGTCAACAATAATAGGGG
CAATAGTCTGACCTTGATTGACCTCCCTGGCCATGAGAGCTTGCGGCTTCAGTTCTTAGAGCGGTTTAAGACTTCAGCCA
GGGCTGTTGTGTTTGTCGTGGATAGTGCAGCATTTCAGAGAGAGGTAAAAGATGTGGCTGAGTTTCTGTATCAAGTCCTC
ATTGACAGCATGAGTCTGAAGAACACACCATCGTTCCTAATAGCCTGCAACAAGCAAGATATTGCAATGGCAAAATCAGC
AAAGTTAATTCAGCAACAGCTTGAGAAAGAACTTAACACCTTATGAGTTACCCGTTCTGCTGCACCCAGTACACTGGACA
GTTCCAGCACTGCCCCTGCTCAACTGGGAAAGAAAGGCAAAGAATTTGAATTCTCACAGTTGCCCCTCAAAGTGGAGTTC
CTGGAGTGTAGTGCCAAGGGTGGGAGAGGGGACCCCGGCTCCGCTGACATCCAGGACCTGGAGAAGTGGCTTGCTAAAAT
CGCC
ORF - retro_ocun_1403 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.25 % |
| Parental protein coverage: | 98.89 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ADSRRLGDGDGAGGAFQPYLDSLRQELQQRDPTVLSVVVALLAVLLTLVFWKLVRSRRSSQRAVLLLGLC |
| ADSRRLGDGDGAGGAFQPYLDSLRQELQQRDPTVLSVVVALLAVLLTLVFWKLV.SRRSSQRAVLLLGLC | |
| Retrocopy | ADSRRLGDGDGAGGAFQPYLDSLRQELQQRDPTVLSVVVALLAVLLTLVFWKLVCSRRSSQRAVLLLGLC |
| Parental | DSGKTLLFVRLLTGHYRDTQTSITDSSATYRVNNNRGNSLTLIDLPGHESLRLQFLERFKTSARAVVFVV |
| DSGKTLLFVRLLTGHYRDTQTSITDSSATYRVNNNRGNSLTLIDLPGHESLRLQFLERFKTSARAVVFVV | |
| Retrocopy | DSGKTLLFVRLLTGHYRDTQTSITDSSATYRVNNNRGNSLTLIDLPGHESLRLQFLERFKTSARAVVFVV |
| Parental | DSAAFQREVKDVAEFLYQVLIDSMSLKNTPSFLIACNKQDIAMAKSAKLIQQQLEKELNTLRVTRSAAPS |
| DSAAFQREVKDVAEFLYQVLIDSMSLKNTPSFLIACNKQDIAMAKSAKLIQQQLEKELNTL.VTRSAAPS | |
| Retrocopy | DSAAFQREVKDVAEFLYQVLIDSMSLKNTPSFLIACNKQDIAMAKSAKLIQQQLEKELNTL*VTRSAAPS |
| Parental | TLDSSSTAPAQLGKKGKEFEFSQLPLKVEFLECSAKGGRGDPGSADIQDLEKWLAKIA |
| TLDSSSTAPAQLGKKGKEFEFSQLPLKVEFLECSAKGGRGDPGSADIQDLEKWLAKIA | |
| Retrocopy | TLDSSSTAPAQLGKKGKEFEFSQLPLKVEFLECSAKGGRGDPGSADIQDLEKWLAKIA |
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 |
|---|---|---|
| SRP017611_brain | 2 .76 RPM | 17 .38 RPM |
| SRP017611_kidney | 3 .65 RPM | 25 .44 RPM |
| SRP017611_liver | 1 .16 RPM | 11 .25 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1403 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1403 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1403 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Microcebus murinus | ENSMICG00000009618 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000007623 | 1 retrocopy |
retro_ocun_1403 ,
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