RetrogeneDB ID: | retro_ocun_1505 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 9:43316017..43318747(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DENND4B | ||
| Ensembl ID: | ENSOCUG00000011771 | ||
| Aliases: | None | ||
| Description: | DENN/MADD domain containing 4B [Source:HGNC Symbol;Acc:29044] |
Retrocopy-Parental alignment summary:
>retro_ocun_1505
GCCTTCCTTACCTTCCTCTACCGCGACTCTGTCTCAGGCCCCCACCGCCTGCCCTTGGAAGCGCACATCTTCCACTTCAT
TCACAACATCGCCTTCCCCTCCCCATAGAGACCCCGCATCCTAGTGCAGATGTCTCCCTACGACAACCTGCTCCTCTGTC
AACCTGTGTCTTCACCCCTGCCCCTCAGCGGTGCCAGCTTCTTGCAGCTGCTGCAGAGCCTGGGCCCTGAGCTGGCTGTC
ATGCTGCTGCTGGCCGTGCTCACGGAGCACAAACTGCTGGTGCACTCGCTGCGGCCAGACCTGCTCACCAGTGTCTGTGA
GGCCCTTGTCTCGATGATCTTTCCGCTGCACTGGCAGTGCCCCTACATTCCGCTGTGCCCGCTGGTGCTGGCAGATGTGC
TGAGCACCCCTGTGCCCTTCATCGTGGGCATCCACTCCAGCTACTTTGATCTGCATGATCCCCCGGCCTACGTCGTCTGT
GCCGACCTTGACACCAACACATTCTGCCAGACCGAGGAAAAGAAGCCCCTCTCCCCTCGGACCCTGCCTCGCAGACCCTA
CAAGCTTCTGCTGGCCACTCTGACTAACCTGTACCAGCAGCTGGACCAGACGTACACTGGACCTGAGCAGGAGGCCTCCC
TGGAATTCCTGCTGACCGACTATGAGGCAGTGTGTGGTCGCTGGGCCGACTGGAGCTAGAGGTCCAAGGCGCCTTCCTCC
GCTTCATGGCCTGCCTGCTCAAGGGCTACCGGGAATTCCTGCGCCCACTCAGCCAGGCCCCCTTGAGGGCGCTCCCACGT
GGACAACTTTTTCTATCTTCATGGCTTCCTGAAGTCCCACGAGCACTCCAGCCACAAGCTGTACTTCCAGCTGCTGCACA
CACAGATGTTCTCCCAGTTCATTGAGGAGTGCTCTTTTGGCTCTGCTCGGCACGCTGCCCTGGAATTCTTTGACTCCGGC
GTCGACGAGGTCCATGCCGAGTAGGAAAGGCCTGAGCCCACTCCGTTAGTGGAGCTGGAAGAGTTGTCGGGAAGTGAGCT
CACAGTCTTCATCACGCCTCCCGAGGAGCCCCCGGTCCCAGACAGCAGCGAACCAACTCCCCAGTTCTGTTACATGGGTT
CCCAGAACTACGGGCTGAGCTGTTTGAATCTCCCCAAGAGCAACCTGGGGCACTGCCTGTGCCGGGCACCTCCAGTAGTG
CCCCCAGCAGTCCTGCCCCTCGCAGTACCAAACAGGAGATGAAGGTTGCACAGCGCATGGCACAGAAGTCAGCGACCGTG
CCTGAGCTGTGGGCCCAGTGCCTGCTGGGGCACTGCTACGGGCTGTGGTTCCTGTGCCTGCCTGCCTACATACAGTCGGC
ACCATCCCAGGTACCAGCACTGAACACAGCCTACCATGTGCTGCGCGAGATGGAGAGCTGTAAAGTGGTGCTCCCTGACG
AGGTGTGTTACCGGGTGCTGATGCAGCTCTGCTCACACTATGGGCAGCCTGTGCTGTCTGTGCGGGTCATGCTGGAGATG
CGGTGGGCGGGCATTTTGCCCAATACCATCACCTGTGGCTACTACAACAAGGCTGTGCTGGAAAGCAAGTGGCTGTGGGC
ACACTGGGTGGGCGCCTGCGCTGGGCCAAGCTCTGGAATGTTGTCCTGGGAGCTACTTAGTTCCACCAACCCCTGAGAGA
GCCATGGCGGCAGCAACAGCAGCCACAGCCAGCGGCAGCACAGCAAGAGGTAGGCAGCTCCCAGACAGAGCCCTGTCTGG
AGCGCCCCTCCCCTACCCGCCCACTCCAGCACCAGACTACCTGGGCTGGGTGAAGTCTGAGGAACCCAGCCTCCCCTGTG
GGGCACCTGATGAAGAGCGGGAGCCTGGGCAGTGCCCGAGGTGCACAGCCCACTGTGGAGGCCGGTGTGGCCCACATGAT
AGAGGCCTTGGGGGTTCTGGAACCCCTCAGCTCACTTGTGCCCTGGCATGGTGGAAGTCTCTCAGACCTGAGCCTTACCG
AGGAGGAGCTGGCACCTGGGGGCAGCCCAGGGGGCTCAGGCCTTGCCCTGAGTGCCCAGTCCACTGAGGCCCTGGAAGGG
CTAAATGGCCGTGGGTCCAAGGCTGGTGGGCATCAGGAGGAGGCGGGCACCCCCCGACGAGGGCTGGGTGCCTGCCTTCA
GCAGCTGCTCACCCCCTCCCATCGCTCCCCTGCCTCCCGCATTCCCCCATCTGAGCTGCCCGCTGACCTGCCACCCCCAG
TTCGCCGCAGCCCCATGGACAGCCTCCTGCACCCCCGGGAGCGCCCTGGATCTACTGCGTCCAAGAGTTCAGCCTCTCTG
GGCAGTGAGTGGGACCTCTCAGACTCTTCTCTCAGCAGCCTGCGCCTCCGCCGTTCCTCAGCGACACCCCTGGGTCCTCC
CAGACACTTTCCCTGGAAATTCTGCTGTCCATCTGCTCCCTGTGCCGTGCCTGTGATTTGCAGGTGTAGGATGAGGAAAT
CATGGCTGGCTGGGCACCGGATGACTCTAACCTCAACACAACCTGTCCCTTCTGCGCCTGTCCCTTCGTGCCCCTGCTCA
GCGTCCAGACCCTTGATTCCCGACCCAGTGCCCCCAGCCCCAAGCCGACCCCTGCTGGTGCCAGTGGCAGCAAAGATGCT
CCCATCCCTGGGGGTCCTGGCCCTGTACTCAGTGACCGGAGGCTCTGCCTCGCCCTGGATGAGCCCCAGCTCTGCAATGG
GCACATGGGG
ORF - retro_ocun_1505 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.53 % |
| Parental protein coverage: | 61.18 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | AFLTFLYRYSVSGPHRLPLEAHISHFIHNVPFPSPQRPRILVQMSPYDNLLLCQPVSSPLPLSGASFLQL |
| AFLTFLYR.SVSGPHRLPLEAHI.HFIHN..FPSP.RPRILVQMSPYDNLLLCQPVSSPLPLSGASFLQL | |
| Retrocopy | AFLTFLYRDSVSGPHRLPLEAHIFHFIHNIAFPSP*RPRILVQMSPYDNLLLCQPVSSPLPLSGASFLQL |
| Parental | LQSLGPELAVTLLLAVLTEHKLLVHSLRPDLLTSVCEALVSMIFPLHWQCPYIPLCPLVLADVLSAPVPF |
| LQSLGPELAV.LLLAVLTEHKLLVHSLRPDLLTSVCEALVSMIFPLHWQCPYIPLCPLVLADVLS.PVPF | |
| Retrocopy | LQSLGPELAVMLLLAVLTEHKLLVHSLRPDLLTSVCEALVSMIFPLHWQCPYIPLCPLVLADVLSTPVPF |
| Parental | IVGIHSSYFDLHDPPADVICVDLDTNTLFQTEEKKPLSPRTLPRRPYKVLLATLTNLYQQLDQTYTGPEQ |
| IVGIHSSYFDLHDPPA.V.C.DLDTNT..QTEEKKPLSPRTLPRRPYK.LLATLTNLYQQLDQTYTGPEQ | |
| Retrocopy | IVGIHSSYFDLHDPPAYVVCADLDTNTFCQTEEKKPLSPRTLPRRPYKLLLATLTNLYQQLDQTYTGPEQ |
| Parental | EASLEFLLTDYEAVCGRRA-RLEREVQGAFLRFMACLLKGYREFLRPLTQA-PSEGA-RDVDNLFHLQGF |
| EASLEFLLTDYEAVCGR.A.RLE.EVQGAFLRFMACLLKGYREFLRPL.QA.P.EGA...VDN.F.L.GF | |
| Retrocopy | EASLEFLLTDYEAVCGRWA<RLELEVQGAFLRFMACLLKGYREFLRPLSQA<PLEGA<SHVDNFFYLHGF |
| Parental | LKSRERSSHKLYSQLLHTQMFSQFIEECSFGSARHAALEFFDSCVDKVHAEQERPEPTPLVELEELSGSE |
| LKS.E.SSHKLY.QLLHTQMFSQFIEECSFGSARHAALEFFDS.VD.VHAE.ERPEPTPLVELEELSGSE | |
| Retrocopy | LKSHEHSSHKLYFQLLHTQMFSQFIEECSFGSARHAALEFFDSGVDEVHAE*ERPEPTPLVELEELSGSE |
| Parental | LTVFITPPEEPPVPDSSEPIPQFCY-DGFPELRAELFESPQEQPGALPVPGTSRSAPSSPAPRRTKQEMK |
| LTVFITPPEEPPVPDSSEP.PQFCY..GFPELRAELFESPQEQPGALPVPGTS.SAPSSPAPR.TKQEMK | |
| Retrocopy | LTVFITPPEEPPVPDSSEPTPQFCY<HGFPELRAELFESPQEQPGALPVPGTSSSAPSSPAPRSTKQEMK |
| Parental | VAQRMAQKSATVPELWARCLLGHCYGLWFLCLPAYVRSAPSRVRALHTAYQVLRQMESRKVVLPDEVCYR |
| VAQRMAQKSATVPELWA.CLLGHCYGLWFLCLPAY..SAPS.V.AL.TAY.VLR.MES.KVVLPDEVCYR | |
| Retrocopy | VAQRMAQKSATVPELWAQCLLGHCYGLWFLCLPAYIQSAPSQVPALNTAYHVLREMESCKVVLPDEVCYR |
| Parental | VLMQLCSHYGQPVLSVRVMLEMRRAGIVPNTITYGYYNKAVLESKW-PSGTPGGRLRWAKLRNVVLGAAQ |
| VLMQLCSHYGQPVLSVRVMLEMR.AGI.PNTIT.GYYNKAVLESKW...GT.GGRLRWAKL.NVVLGA.. | |
| Retrocopy | VLMQLCSHYGQPVLSVRVMLEMRWAGILPNTITCGYYNKAVLESKW<AVGTLGGRLRWAKLWNVVLGAT* |
| Parental | FRQPLKERRRQQQQQQQQPAAQQEAGSSQTGGWGQTEPCLERPSPTRPLQRQTTWAGRSLRDPASPAGRL |
| F.QPL.E..R....QQQQP...Q.A...Q..G..QTEPCLERPSPTRPLQ.QTTWAG.SLR.PASP.G.L | |
| Retrocopy | FHQPLREPWR----QQQQP---QPAAAQQEVGSSQTEPCLERPSPTRPLQHQTTWAG*SLRNPASPVGHL |
| Parental | VKSGSLGSARGAQPTVEAGVAHMIEALGVLEPRGSPVPWHDGSLSDLSLTGEELAPGGSPGGSGPALSAQ |
| .KSGSLGSARGAQPTVEAGVAHMIEALGVLEP..S.VPWH.GSLSDLSLT.EELAPGGSPGGSG.ALSAQ | |
| Retrocopy | MKSGSLGSARGAQPTVEAGVAHMIEALGVLEPLSSLVPWHGGSLSDLSLTEEELAPGGSPGGSGLALSAQ |
| Parental | STEALEGLSGRGPKAAGHQEEAGTPRRGLGARLQQLLTPSRRSPASRIPPPELPADLPPPARRSPMDSLL |
| STEALEGL.GRG.KA.GHQEEAGTPRRGLGA.LQQLLTPS.RSPASRIPP.ELPADLPPP.RRSPMDSLL | |
| Retrocopy | STEALEGLNGRGSKAGGHQEEAGTPRRGLGACLQQLLTPSHRSPASRIPPSELPADLPPPVRRSPMDSLL |
| Parental | HPRERPGSTASESSASLGSEWDLSESSLSSLSLRRSSER-LSDTPGSSQPPSLEILLSSCSLCRACDSLV |
| HPRERPGSTAS.SSASLGSEWDLS....SSLS..R.....LSDTPGSSQ..SLEILLS.CSLCRACD..V | |
| Retrocopy | HPRERPGSTASKSSASLGSEWDLSD---SSLSSLRLRRS<LSDTPGSSQTLSLEILLSICSLCRACDLQV |
| Parental | YDEEIMAGWAPDDSNLNTTCPFCACPFVPLLSVQTLDSRPSAPSPKPTPAGASGSRDAPVPGGPGPVLSD |
| .DEEIMAGWAPDDSNLNT............LSVQTLDSRPSAPSPKPTPAGASGS.DAP.PGGPGPVLSD | |
| Retrocopy | *DEEIMAGWAPDDSNLNTXXXXXXXXXXXXLSVQTLDSRPSAPSPKPTPAGASGSKDAPIPGGPGPVLSD |
| Parental | RRLCLALDEPQLCNGHMG |
| RRLCLALDEPQLCNGHMG | |
| Retrocopy | RRLCLALDEPQLCNGHMG |
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 .33 RPM | 60 .38 RPM |
| SRP017611_kidney | 0 .10 RPM | 18 .04 RPM |
| SRP017611_liver | 0 .00 RPM | 13 .49 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1505 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1505 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1505 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 | ENSOCUG00000011771 | 1 retrocopy |
retro_ocun_1505 ,
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