RetrogeneDB ID: | retro_ocun_1684 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018762:550877..551704(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSOCUG00000027138 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZDHHC2 | ||
| Ensembl ID: | ENSOCUG00000014585 | ||
| Aliases: | None | ||
| Description: | zinc finger, DHHC-type containing 2 [Source:HGNC Symbol;Acc:18469] |
Retrocopy-Parental alignment summary:
>retro_ocun_1684
AGAGAAAGAATTGTTGGAGAACCAAGAGGACAACCCCATCAGGAAGTTCTTAGGCGAGCAGCCAAGGATCTTCCCATTTT
TACCAGGACCATGACTGGAGCCATCCGCTACTGTGACAGATGCCAACTTATAAAACCAGATCACTGCCATCATTGTTCCA
TCTGCAATAAATGTATTTTGAAGATGGATCATCATTGCCCATGGGTGAACAATTGTGTGGGAATTTCAGATTATAAATTC
TTCCTCCTTTTCCTGGCTTATTATCTGCTGTACTGCCTTTTTATCACTGCTACAGACTTACAGTATATTGTCAAATTTTG
GACAAGTGGTCTACCAGAGACTCAAGCCAAGTTCCATATGCTGTTTCTATTCTTTGCTGCAGCTAGTTTTCTGTCAGTTT
ATCTTCTCTATTTGGCTATCATTGTTGGCTAGTCGGCAAAAATAAATCTACATTAGAGGCATTCAGGAGTCCAGTATCTT
GACATGGAACCAATAAGAATGGATTCAGCTTAGGTCTCAGTAAAAATAATGAGACAAGTTTTTGGTGATGAGAAGAAGTA
CTGGTTGTTACCCATTTTTTCACATCTGTCTGATGGCTGTTCCTTCCCAACTTGCCTTGTTAACCAGGATCCTGAACAAC
CATCTACTCCTGCAGGACTGAATTCAACAGCTAAAAATCCTGAAAACCATCAGTTCCTGCAAATCCATAGAGAGAATTCC
AGAGCCACCTTCTCACTGACTCGCAGTCTTGGACAGAAAGCAACATAAGCCCTGGAAGAGGCAAAGATCCTATGAGCAAT
CCTGTATTAACCATGGAGAATGAGACT
ORF - retro_ocun_1684 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.3 % |
| Parental protein coverage: | 83.64 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | KELLEREPRGEAHQEVLRRAARDLPIYTRTMSGAIRYCDRCQLIKPDRCHHCSVCDKCILKMDHHCPWVN |
| .E....EPRG..HQEVLRRAA.DLPI.TRTM.GAIRYCDRCQLIKPD.CHHCS.C.KCILKMDHHCPWVN | |
| Retrocopy | RERIVGEPRGQPHQEVLRRAAKDLPIFTRTMTGAIRYCDRCQLIKPDHCHHCSICNKCILKMDHHCPWVN |
| Parental | NCVGFSNYKFFLLFLAYSLLYCLFIAATDLQYFVKFWTNGLPDTQAKFHIMFLFFAAAM-FSVSLSSLFG |
| NCVG.S.YKFFLLFLAY.LLYCLFI.ATDLQY.VKFWT.GLP.TQAKFH..FLFFAAA..FSVSLSSLFG | |
| Retrocopy | NCVGISDYKFFLLFLAYYLLYCLFITATDLQYIVKFWTSGLPETQAKFHMLFLFFAAAS<FSVSLSSLFG |
| Parental | YHCWLVSKNKSTLEAFRSPVFRHGTDKNGFSLGFSKN-MRQVFGDEKKYWLLPIFSSLGDGCSFPTCLVN |
| YHCWLV.KNKSTLEAFRSPV..HGT.KNGFSLG.SKN.MRQVFGDEKKYWLLPIFS.L.DGCSFPTCLVN | |
| Retrocopy | YHCWLVGKNKSTLEAFRSPVS*HGTNKNGFSLGLSKN>MRQVFGDEKKYWLLPIFSHLSDGCSFPTCLVN |
| Parental | QDPEQPSTPAGLNSTTKNPENHQF-PAKPLRESQSHLLTDSQSWTESNINPGRGKAGMSNPALTMENET |
| QDPEQPSTPAGLNST.KNPENHQF.PA.P.RE.QSHLLTDSQSWTESNI.PGRGK..MSNP.LTMENET | |
| Retrocopy | QDPEQPSTPAGLNSTAKNPENHQF<PANP*REFQSHLLTDSQSWTESNISPGRGKDPMSNPVLTMENET |
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 .28 RPM | 29 .69 RPM |
| SRP017611_kidney | 0 .00 RPM | 8 .01 RPM |
| SRP017611_liver | 0 .00 RPM | 1 .00 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1684 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1684 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1684 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000011824 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000014585 | 2 retrocopies |
retro_ocun_1684 , retro_ocun_1725,
|