RetrogeneDB ID: | retro_ocun_364 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 1:56032379..56033113(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAP1GAP2 | ||
| Ensembl ID: | ENSOCUG00000000200 | ||
| Aliases: | None | ||
| Description: | RAP1 GTPase activating protein 2 [Source:HGNC Symbol;Acc:29176] |
Retrocopy-Parental alignment summary:
>retro_ocun_364
AGACAACAAGATGAACTAAATCAAGCTATAGCAGGGTATCATTATTCAAGTGGCTAAGAAGAGGCACATGAAGCTTTTAA
AAAGGAAACTGAACTAGATATAAATGAGGAATTAAATAAGAAGCATACTGGTCTTCTGGAAAAAAATGGAATTCTGTTAC
TAGATTGCAAAAGAAGGTTATGGAATTAGAATCAAAACTAAATGAAGCAAAAGAAGAATATACATCGGGTGGACCTCTTG
GTCAGAAAAGAGACCCAAAAGAATGGATTCCCCATCCACCAGAAAAATGCACTTTGCGTGGTCACAGGAGTCCAGTCAAC
TTGAGTCATATTCCATCCTGTGTTCAGTGTTATGGTCTCTGTGTCTGAGGATGCTACAATTTAGGTGTGGGATTATGAGA
TTGGTGATTTTGAATGAAGTATTAAGGGGCATATAGATTCTGTACTGGACATTTCTTTTGACCCCAGAGGCAAGCTATGG
CTTCCTGTTCTGCATAGAGGACCACAAAACTATAAAATTTTCAGGGCTTTGAAGGCATCAGAACTATGCATGAGCACAAC
CACAATGTCTCTTCAGTAGCCATCGTGCCCAGTGGAGATCATGTAGTGTCTACTTCAAGAGATAAAACTATACAAATGTG
GAAAGTGCAAACTGGCTACTGTGTGAAGACATTCACAGGACACAGAGAATGGACACATACAATACAGCCAAGTCAGGATG
GCACTCTGATAGCT
ORF - retro_ocun_364 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.02 % |
| Parental protein coverage: | 59.76 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | RQRDELNRAIADYLRSNGYEEAYSVFKKEAELDMNEELDKKYAGLLEK-KWTSVIRLQKKVMELESKLNE |
| RQ.DELN.AIA.Y..S.G.EEA...FKKE.ELD.NEEL.KK..GLLEK.KW.SV.RLQKKVMELESKLNE | |
| Retrocopy | RQQDELNQAIAGYHYSSG*EEAHEAFKKETELDINEELNKKHTGLLEK<KWNSVTRLQKKVMELESKLNE |
| Parental | AKEEFTSGGPLGQKRDPKEWIPRPPEKYALSGHRSPV-TRVIFHPVFSVMVSASEDATIKVWDYETGDFE |
| AKEE.TSGGPLGQKRDPKEWIP.PPEK..L.GHRSPV.T.VIFHPVFSVMVS.SEDATI.VWDYE.GDFE | |
| Retrocopy | AKEEYTSGGPLGQKRDPKEWIPHPPEKCTLRGHRSPV>T*VIFHPVFSVMVSVSEDATI*VWDYEIGDFE |
| Parental | RTLKGHTDSVQDISFDHSGKL-LASCSADMTIKLWDFQGFECIRTMHGHDHNVSSVAIMPNGDHIVSASR |
| ...KGH.DSV.DISFD..GKL..ASCSA..T.KL..FQGFE.IRTMH.H.HNVSSVAI.P.GDH.VS.SR | |
| Retrocopy | *SIKGHIDSVLDISFDPRGKL<MASCSA*RTTKL*NFQGFEGIRTMHEHNHNVSSVAIVPSGDHVVSTSR |
| Parental | DKTIKMWEVQTGYCVKTFTGHREWVRMVRPNQDGTLIA |
| DKTI.MW.VQTGYCVKTFTGHREW.....P.QDGTLIA | |
| Retrocopy | DKTIQMWKVQTGYCVKTFTGHREWTHTIQPSQDGTLIA |
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 | 312 .26 RPM |
| SRP017611_kidney | 0 .00 RPM | 104 .90 RPM |
| SRP017611_liver | 0 .00 RPM | 35 .30 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_364 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_364 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_364 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 | ENSOCUG00000000200 | 1 retrocopy |
retro_ocun_364 ,
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