RetrogeneDB ID: | retro_ocun_1776 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018886:489991..490365(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAB23 | ||
| Ensembl ID: | ENSOCUG00000004816 | ||
| Aliases: | None | ||
| Description: | RAB23, member RAS oncogene family [Source:HGNC Symbol;Acc:14263] |
Retrocopy-Parental alignment summary:
>retro_ocun_1776
GTCAAGATGGTGGTTGTAGGGAATGGAACAGTTGGAAAGTCAAGTATGATTCAGCAATATTGCAAATGCATTTTTATAAA
AGACTACAAGAAAACCTTGGAGTTGATTTTTTGGAGCAACAAATCCAAGTTATTGATGAAGATGTCAGATTGATGTTATG
GGATACTGCTGGTCAAAAGGAATTTGATACAATAATGAATGCCTATTATCCAGGAGCCCAGACTTGTGTGCTTATATTTT
CTACTACAGACAGGGAATCTTTTGAAACAATTTCCAGTTGGAGAGAGAAAGTCGGAGCTGAAGTTGGGGATATATGAACT
GTACTTGTAAAAAATAAGATTGATTTCTTGGATGATTCTTGTACAAAGAATGAG
ORF - retro_ocun_1776 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.54 % |
| Parental protein coverage: | 52.74 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | IKMVVVGNGAVGKSSMIQRYCKGIFTKDYKKTI-GVDFLERQIQVNDEDVRLMLWDTAGQEEFDAITKAY |
| .KMVVVGNG.VGKSSMIQ.YCK.IF.KDYKKT..GVDFLE.QIQV.DEDVRLMLWDTAGQ.EFD.I..AY | |
| Retrocopy | VKMVVVGNGTVGKSSMIQQYCKCIFIKDYKKTL<GVDFLEQQIQVIDEDVRLMLWDTAGQKEFDTIMNAY |
| Parental | YRGAQACVLVFSTTDRESFEAISSWREKVVAEVGDIPTVLVQNKIDLLDDSCIKNE |
| Y.GAQ.CVL.FSTTDRESFE.ISSWREKV.AEVGDI.TVLV.NKID.LDDSC.KNE | |
| Retrocopy | YPGAQTCVLIFSTTDRESFETISSWREKVGAEVGDI*TVLVKNKIDFLDDSCTKNE |
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 | 10 .54 RPM |
| SRP017611_kidney | 0 .00 RPM | 11 .96 RPM |
| SRP017611_liver | 0 .00 RPM | 1 .23 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1776 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1776 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1776 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000004816 | 2 retrocopies |
retro_ocun_1752, retro_ocun_1776 ,
|
| Oryctolagus cuniculus | ENSOCUG00000026506 | 2 retrocopies |