RetrogeneDB ID: | retro_ocun_662 | ||
Retrocopylocation | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 13:102154108..102154641(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSOCUG00000003109 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | CENPM | ||
| Ensembl ID: | ENSOCUG00000008255 | ||
| Aliases: | None | ||
| Description: | centromere protein M [Source:HGNC Symbol;Acc:18352] |
Retrocopy-Parental alignment summary:
>retro_ocun_662
ATGTTGGTGTTAAGGCCGCTAGACAAGCTGCCCGGCCTGAACACGGCCACCCTCTTGCTGGTGGGCACAGACGATGCTCT
TCTGCAGCAGCGGGCGGACTCCAGGCTCAAGATGGACTGCGCCTCGGAGCTGAGGGTCCACCTTGCAAGGTCCCTCCCTC
TGCCCTCCAACGTGAATCGGCCTCTGGTGGACCTGCTCGTATTTGTGATTAATCTTCACAGCAAATACAGCCTGCAGAGC
GTGGAGAAGTCCCTGTACCACGTGGACGCCAGCTTCTTCCTAGGGAAGGCGTGCTTCCTGGCCGCAGGCGCTGGGCGGGA
GAGCCACTGCAGCGTTCATCGGAACACCATCATGAGGCTGGCGCACACCTACCGAAGCCCCGTGCTGTTCTGTGACCTGG
AGGTGGAAGGCTTCCGAGCCACCATGGCGCAGCGCCTGGTACGCATGCTGCAGATCTGTGCTGGCCACATGCCCAGCGTC
TCGGCCTGAGCCTGCTGTCCCTGCTCAGGAGCTCCGAGAGCCCCTCCCTGAAG
ATGTTGGTGTTAAGGCCGCTAGACAAGCTGCCCGGCCTGAACACGGCCACCCTCTTGCTGGTGGGCACAGACGATGCTCT
TCTGCAGCAGCGGGCGGACTCCAGGCTCAAGATGGACTGCGCCTCGGAGCTGAGGGTCCACCTTGCAAGGTCCCTCCCTC
TGCCCTCCAACGTGAATCGGCCTCTGGTGGACCTGCTCGTATTTGTGATTAATCTTCACAGCAAATACAGCCTGCAGAGC
GTGGAGAAGTCCCTGTACCACGTGGACGCCAGCTTCTTCCTAGGGAAGGCGTGCTTCCTGGCCGCAGGCGCTGGGCGGGA
GAGCCACTGCAGCGTTCATCGGAACACCATCATGAGGCTGGCGCACACCTACCGAAGCCCCGTGCTGTTCTGTGACCTGG
AGGTGGAAGGCTTCCGAGCCACCATGGCGCAGCGCCTGGTACGCATGCTGCAGATCTGTGCTGGCCACATGCCCAGCGTC
TCGGCCTGAGCCTGCTGTCCCTGCTCAGGAGCTCCGAGAGCCCCTCCCTGAAG
ORF - retro_ocun_662 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.15 % |
| Parental protein coverage: | 98.89 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSVLRPLDKLPGLNTATVLLVGADDALLQRLADSMLKTDCASELRVHLARSLPLPSNVNRPRVDLLVFVI |
| M.VLRPLDKLPGLNTAT.LLVG.DDALLQ..ADS.LK.DCASELRVHLARSLPLPSNVNRP.VDLLVFVI | |
| Retrocopy | MLVLRPLDKLPGLNTATLLLVGTDDALLQQRADSRLKMDCASELRVHLARSLPLPSNVNRPLVDLLVFVI |
| Parental | NLHSKYSLQSVEKSLHHVDASFFLGKACFLATGAGRENLCSVHRNTIVRLARTYRSPVLFCDLEVEGSRA |
| NLHSKYSLQSVEKSL.HVDASFFLGKACFLA.GAGRE..CSVHRNTI.RLA.TYRSPVLFCDLEVEG.RA | |
| Retrocopy | NLHSKYSLQSVEKSLYHVDASFFLGKACFLAAGAGRESHCSVHRNTIMRLAHTYRSPVLFCDLEVEGFRA |
| Parental | AMAQRLARMLQISAGHVPGVSA-MSLLSLLRSSESPSLE |
| .MAQRL.RMLQI.AGH.P.VSA..SLLSLLRSSESPSL. | |
| Retrocopy | TMAQRLVRMLQICAGHMPSVSA<LSLLSLLRSSESPSLK |
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 | 0 .00 RPM | 0 .39 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .71 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_662 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_662 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_662 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000008255 | 1 retrocopy |
retro_ocun_662 ,
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