RetrogeneDB ID: | retro_ocun_1121 | ||
Retrocopylocation | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 2:142669652..142670179(-) | ||
| Located in intron of: | ENSOCUG00000001048 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | C14orf164 | ||
| Ensembl ID: | ENSOCUG00000021958 | ||
| Aliases: | None | ||
| Description: | chromosome 14 open reading frame 164 [Source:HGNC Symbol;Acc:20438] |
Retrocopy-Parental alignment summary:
>retro_ocun_1121
GTCACTCTGGAAAAATGTGCTGTTTCAAGGAACGTCTGCAATCACTCTGCTCTTTCTGATAATCTGAAACCTCAGGAGAC
GGTCTTCAAAACGCCACGAGAAAACAACTTCGCAGTGTTTCAGTCACACCTCTGGGGTCTGGAGTTTCCAAAAGAAACAG
ATCTCATCATCTTTTATAAGCACAGAATTACACAGGCAGAAGTAGCCATGCAAGAGGCAGAGCAGACAGTGGCTAGCCAG
CCAGGACAAACCACTGTCAATCTTAAGAAAGGAGAACAGAGAATGGAAGAAATGTGTAACCACCCCAAAGGAACCTGCAA
GTCAGCACCAGGGAAGCAGGCTGAGCACACTGCAGCCGGTAGACGTTACTTTCCCATCACAGTCAGTTACTTCAAAACTC
GGTTCCTGCCACAGTAGCCGAGTGGTCAGTCAGTTCTCGGTGCAGTCTATCCCTTAGAAGAAGGCTGGCTTTGGAAGCCT
GAGACAGGAAGTGGGTGCCTCAGGGAAAGAGCACTCCAAAAAACGCC
GTCACTCTGGAAAAATGTGCTGTTTCAAGGAACGTCTGCAATCACTCTGCTCTTTCTGATAATCTGAAACCTCAGGAGAC
GGTCTTCAAAACGCCACGAGAAAACAACTTCGCAGTGTTTCAGTCACACCTCTGGGGTCTGGAGTTTCCAAAAGAAACAG
ATCTCATCATCTTTTATAAGCACAGAATTACACAGGCAGAAGTAGCCATGCAAGAGGCAGAGCAGACAGTGGCTAGCCAG
CCAGGACAAACCACTGTCAATCTTAAGAAAGGAGAACAGAGAATGGAAGAAATGTGTAACCACCCCAAAGGAACCTGCAA
GTCAGCACCAGGGAAGCAGGCTGAGCACACTGCAGCCGGTAGACGTTACTTTCCCATCACAGTCAGTTACTTCAAAACTC
GGTTCCTGCCACAGTAGCCGAGTGGTCAGTCAGTTCTCGGTGCAGTCTATCCCTTAGAAGAAGGCTGGCTTTGGAAGCCT
GAGACAGGAAGTGGGTGCCTCAGGGAAAGAGCACTCCAAAAAACGCC
ORF - retro_ocun_1121 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.37 % |
| Parental protein coverage: | 60.47 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VTLEKCAVCGTACKHLALSDNLKPQEKMFFRSPVETALQYFNHISQVWSFQ-KKQTDLLIAFQKHRITKL |
| VTLEKCAV....C.H.ALSDNLKPQE..F...P.E.....F...S..W.....K.TDL.I.F.KHRIT.. | |
| Retrocopy | VTLEKCAVSRNVCNHSALSDNLKPQETVF-KTPRENNFAVFQ--SHLWGLEFPKETDLII-FYKHRITQA |
| Parental | EAAMQEAQQTMASQDKELSM-LK-KENGELKKYLALLKESPSRYQGSRLTTPRPVGITSPTQSVTPRPSC |
| E.AMQEA.QT.ASQ.......LK.KEN.E.KK.....KE..S..QGSRL.T..PV..T.P.QSVT..... | |
| Retrocopy | EVAMQEAEQTVASQPGQTTVNLK>KENREWKKCVTTPKEPASQHQGSRLSTLQPVDVTFPSQSVTSKLGS |
| Parental | HHSSQVVSRSSSVESIPYRVADFGSIGQQGRGLQG-RSTPRDS |
| .HSS.VVS...SV.SIP...A.FGS..Q...G..G..STP... | |
| Retrocopy | CHSSRVVSQ-FSVQSIP*KKAGFGSLRQE-VGASG>KSTPKNA |
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 .11 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .41 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .39 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1121 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1121 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1121 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 | ENSOCUG00000021958 | 1 retrocopy |
retro_ocun_1121 ,
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