RetrogeneDB ID: | retro_ocun_563 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 12:57691706..57692451(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | UBXN2B | ||
| Ensembl ID: | ENSOCUG00000023461 | ||
| Aliases: | None | ||
| Description: | UBX domain protein 2B [Source:HGNC Symbol;Acc:27035] |
Retrocopy-Parental alignment summary:
>retro_ocun_563
AAGTTTTATTCAGGTGAACATGAATACGGTGGATTACATATAGTTCAACTTCAACTGGGAAAATTGTGAGTAAACTTTTC
AAAGAGGCAAGGGAGCATGGGGCTGTCCTCTGAATGAAGCCACTAGATCTTCAAGTGATGACAAATATAAGTCCTTTCCA
GGTGGAGGATACAGATTGGGAAATTCCTTTTGTAAGCAGTCTGAATACATCTATGGAGAAAATCAGCTGCAAGGTGTTCA
GATTTTGCTTAACCTATGGAGCAATGGTTTCAGCTTAGATGATGGAGAATTGAAACGTTACTGTGACCCAGTAAATGCTC
AATTTTGGGAGTCTTAAAAGAGGAGAGATTCCTTTGGAGCTTCAGTGAATGATTCATGGGGGCCAACTGAGTTTGGATGT
GGAGGATCATCAGGATCAAGAATATATAAAACCTACAATGAGGTGCAATGCTTTCAGTGGGGAAGGGCAAAACCTTGGAC
ACCTTACCCTGCAATAGTCAGAACACCTTCCTCTCCAGAAGAGGATAAGTCAGTGCTTAATTCAGTTATTCATATTAATG
ATTCAGTGCCAACAACAAAAATTCAAATCAGATTAGCAGATGGGAGTCATTTGATACAAAGATTCAACAGTATACACAGA
ATCCTGGATGTCCGGGACTTTATTGTACAGTCTCGTCCTGAATTTGCAGCTCTTTACTTTATTCTTGTGACTTCATTTCC
AAATAAAGATCTAACAGATGAAAAC
ORF - retro_ocun_563 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.69 % |
| Parental protein coverage: | 75.83 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | RFYSGEHEYRGLHIVR-PSTGKIVNELFKEAREHGAV-PLNEATRSSSDDKSKSFTGGGYRLGNSFCKRS |
| .FYSGEHEY.GLHIV...STGKIV..LFKEAREHGAV.PLNEATRSSSDDK.KSF.GGGYRLGNSFCK.S | |
| Retrocopy | KFYSGEHEYGGLHIVQ<TSTGKIVSKLFKEAREHGAV<PLNEATRSSSDDKYKSFPGGGYRLGNSFCKQS |
| Parental | EYIYGENQLQDVQVLLKLWSNGFSLDDGELRPYSD-PTNAQFLE-SVKRGEIPLELQRLVHEGQLSLDME |
| EYIYGENQLQ.VQ.LL.LWSNGFSLDDGEL..Y.D.P.....L..S.KRGEIPLELQ...H.GQLSLD.E | |
| Retrocopy | EYIYGENQLQGVQILLNLWSNGFSLDDGELKRYCD<PSKCSILG<SLKRGEIPLELQ*MIHGGQLSLDVE |
| Parental | DHQDQEYVKPRLRFKAFSGEGQKLGSLT-PEIVSTPSSPEEEDKSILNAVVHIDDSVPTTKIQIRLADGS |
| DHQDQEY.KP..R..AFSGEGQ.LG.LT.P.IV.TPSSPEE.DKS.LN.V.HI.DSVPTTKIQIRLADGS | |
| Retrocopy | DHQDQEYIKPTMRCNAFSGEGQNLGHLT<PAIVRTPSSPEE-DKSVLNSVIHINDSVPTTKIQIRLADGS |
| Parental | RLIQRFNCTHRILDVRNFIVQSRPEFAALDFILVTSFPNKDLTDES |
| .LIQRFN..HRILDVR.FIVQSRPEFAAL.FILVTSFPNKDLTDE. | |
| Retrocopy | HLIQRFNSIHRILDVRDFIVQSRPEFAALYFILVTSFPNKDLTDEN |
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 | 5 .96 RPM |
| SRP017611_kidney | 0 .00 RPM | 9 .93 RPM |
| SRP017611_liver | 0 .00 RPM | 2 .77 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_563 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_563 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_563 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 | ENSOCUG00000008783 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000023461 | 1 retrocopy |
retro_ocun_563 ,
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