RetrogeneDB ID: | retro_ocun_1725 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018825:733075..733950(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
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_1725
TATATATTACCAATGGATCCTTCCAAAGAATTCCATCTCTCTTATGCAGAGAAAGAATTGTTGGAGAGAGACCCAAGAGG
ACAACCCCATCAGAAGGTTCTTAGGCGAGCAGCCAGGGATCTTCCCATTTATACCAGGACCATGACTGGAGCCATCCGCT
ACTGTGACAGATGCCAACTTATAAAACCAGATCACTGCCATCACTGTTCCGTCTGCGATAAATGTATTTTGAAGATGGAT
CATCATTGCCCATGGGTGAACAATTGTGTGGGAATTTCAGATTATAAATTCTTCCTCCTTTTCATGGCTTATTATCTGCT
GTACTGCCTTTTTATCACTGCTACAGACTTACAGTATGTTGTCAAATTTTGGACAAGTGGTCTACCAGATACTCAAGCCA
AGTTCCATATGCTGTTTCTATTCTTTGCTGCAGCTAGTTTTCTGTCAGCTTATCTTCTCTATTTGGCTATCATTGTTGGC
TAGTCAGCAAAAATAAATCTACATTAGAGGCATTCAGGAGTCCAGTATCTCGACATGGAACCAATAAGAATGGATTCAGC
TTAGGTCTCAGTAAAAATAATGAGACAAGTTTTTGGTGATGAGAAGTACTGGTTGTTACCCATTTTTTCACATCTGTCTG
ATGGCTGCTCCTTCCCAACTTGCCTTGTTAACCAGGATCCTGAACAACCATCTACTCCTGCAGGACTGAATTCAACAGCT
AAAAATCCTGAAAACCATCAGTTCCTGCAAATCCATTGAGAGAATTCCAGAGCCACCTTCTCACTGACTCTCAGTCTTGG
ACAGAAAGCAACGTAAGCCCTGGAAGAGGCAAAGCTGCTATGAGCAATCCTGCATTAACCATGGAGAATGAGACT
ORF - retro_ocun_1725 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.51 % |
| Parental protein coverage: | 88.79 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | FTLPMNPSKEFHLSYAEKELLEREPRGEAHQEVLRRAARDLPIYTRTMSGAIRYCDRCQLIKPDRCHHCS |
| ..LPM.PSKEFHLSYAEKELLER.PRG..HQ.VLRRAARDLPIYTRTM.GAIRYCDRCQLIKPD.CHHCS | |
| Retrocopy | YILPMDPSKEFHLSYAEKELLERDPRGQPHQKVLRRAARDLPIYTRTMTGAIRYCDRCQLIKPDHCHHCS |
| Parental | VCDKCILKMDHHCPWVNNCVGFSNYKFFLLFLAYSLLYCLFIAATDLQYFVKFWTNGLPDTQAKFHIMFL |
| VCDKCILKMDHHCPWVNNCVG.S.YKFFLLF.AY.LLYCLFI.ATDLQY.VKFWT.GLPDTQAKFH..FL | |
| Retrocopy | VCDKCILKMDHHCPWVNNCVGISDYKFFLLFMAYYLLYCLFITATDLQYVVKFWTSGLPDTQAKFHMLFL |
| Parental | FFAAAM-FSVSLSSLFGYHCWLVSKNKSTLEAFRSPVFRHGTDKNGFSLGFSKN-MRQVFGDEKKYWLLP |
| FFAAA..FSVSLSSLFGYHCWLVSKNKSTLEAFRSPV.RHGT.KNGFSLG.SKN.MRQVFGDE.KYWLLP | |
| Retrocopy | FFAAAS<FSVSLSSLFGYHCWLVSKNKSTLEAFRSPVSRHGTNKNGFSLGLSKN>MRQVFGDE-KYWLLP |
| Parental | IFSSLGDGCSFPTCLVNQDPEQPSTPAGLNSTTKNPENHQF-PAKPLRESQSHLLTDSQSWTESNINPGR |
| IFS.L.DGCSFPTCLVNQDPEQPSTPAGLNST.KNPENHQF.PA.PLRE.QSHLLTDSQSWTESN..PGR | |
| Retrocopy | IFSHLSDGCSFPTCLVNQDPEQPSTPAGLNSTAKNPENHQF<PANPLREFQSHLLTDSQSWTESNVSPGR |
| Parental | GKAGMSNPALTMENET |
| GKA.MSNPALTMENET | |
| Retrocopy | GKAAMSNPALTMENET |
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 | 29 .69 RPM |
| SRP017611_kidney | 0 .00 RPM | 8 .01 RPM |
| SRP017611_liver | 0 .08 RPM | 1 .00 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1725 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1725 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1725 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 ,
|