RetrogeneDB ID: | retro_ocun_1552 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018699:9342405..9343187(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSOCUG00000017167 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CALB1 | ||
| Ensembl ID: | ENSOCUG00000006341 | ||
| Aliases: | None | ||
| Description: | calbindin 1, 28kDa [Source:HGNC Symbol;Acc:1434] |
Retrocopy-Parental alignment summary:
>retro_ocun_1552
ATTGCAGAATCCCACCTGCAATCATCCCTGATCACAGCCTCACAGTTTTTCGAGATCTGGCTTCATTAGGACGCTGATGG
AAGTGGTTACCTGGAGGGAATGGAGCTGCAGAACTTGATCCAGGAGCTCCAGCAGGTGCGAAAGAAGGCTGGGTTGGAAT
TATCACCTGAGATGAAAACTTTTGTGGATCAGTATGGGCAGAGAGATGATGGAAAAAAAGGAATTGTAGAGTTGGCCCAT
GTATTACCCACAGAAGAGAATTTCTTGCTGCTCTTCCGGTGCCAGCAGCTGAAGTCCTGTGAGGAATTCATGAAGACATG
GAGAAAATGTGATACTGAACACAGTGGCTTCATAGAAACTGAGGAACTTAAGAACTTTCTAAAGGATCTGCTGGAAAAAG
CAAACAAGACGGTAGATGACACAAAATTAGCTGAGTATACAGACCTAATGCTGAAACTATTTGATTCAAATAATCATGGG
AAGCTGGAATTAACTGAGATGGCCAGGTTATCACCAGTGCAAGAGAATTTTCTTCTTAACTTTCAGGGAATCAAAATGTG
TGGGAAAGAGTTCAATAAGGCTTTGAGTTATAAGATCAGGATGGTAACGGGTACATAGATGAAAATGAACTGGATGCCTT
ACTGAAGGATCTGTGTGAGAAGAATAAACAGGAACTGGATATTAATAATATTCCAACATACAAGAAGAGCATAATGGCTT
TGTCGGATTGAGGGAAGCTCTACGGAACAGATCTTGCTCTTATTCTTTGTGCTGGATACAAC
ORF - retro_ocun_1552 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.3 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAESHLQSSLITASQFFEIWLHYDADGSGYLEGMELQNLIQELQQARKKAGLELSPEMKTFVDQYGQRDD |
| .AESHLQSSLITASQFFEIWLH.DADGSGYLEGMELQNLIQELQQ.RKKAGLELSPEMKTFVDQYGQRDD | |
| Retrocopy | IAESHLQSSLITASQFFEIWLH*DADGSGYLEGMELQNLIQELQQVRKKAGLELSPEMKTFVDQYGQRDD |
| Parental | GKIGIVELAHVLPTEENFLLLFRCQQLKSCEEFMKTWRKYDTDHSGFIETEELKNFLKDLLEKANKTVDD |
| GK.GIVELAHVLPTEENFLLLFRCQQLKSCEEFMKTWRK.DT.HSGFIETEELKNFLKDLLEKANKTVDD | |
| Retrocopy | GKKGIVELAHVLPTEENFLLLFRCQQLKSCEEFMKTWRKCDTEHSGFIETEELKNFLKDLLEKANKTVDD |
| Parental | TKLAEYTDLMLKLFDSNNDGKLELTEMARRLLPVQENFLLKFQGIKMCGKEFNKA-FELYDQDGNGYIDE |
| TKLAEYTDLMLKLFDSNN.GKLELTEMA.RL.PVQENFLL.FQGIKMCGKEFNKA.FEL.DQDGNGYIDE | |
| Retrocopy | TKLAEYTDLMLKLFDSNNHGKLELTEMA-RLSPVQENFLLNFQGIKMCGKEFNKA<FEL*DQDGNGYIDE |
| Parental | NELDALLKDLCEKNKQELDINNIPTYKKSIMALSDGGKLYRTDLALILCAGDN |
| NELDALLKDLCEKNKQELDINNIPTYKKSIMALSD.GKLY.TDLALILCAG.N | |
| Retrocopy | NELDALLKDLCEKNKQELDINNIPTYKKSIMALSD*GKLYGTDLALILCAGYN |
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 | 4 .86 RPM | 278 .70 RPM |
| SRP017611_kidney | 8 .62 RPM | 454 .38 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .23 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1552 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1552 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1552 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 | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000006341 | 1 retrocopy |
retro_ocun_1552 ,
|
| Tupaia belangeri | ENSTBEG00000005714 | 1 retrocopy |