RetrogeneDB ID: | retro_ocun_1670 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018752:622610..623318(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PHF6 | ||
| Ensembl ID: | ENSOCUG00000007022 | ||
| Aliases: | None | ||
| Description: | PHD finger protein 6 [Source:HGNC Symbol;Acc:18145] |
Retrocopy-Parental alignment summary:
>retro_ocun_1670
TATTGCCAAAAACATAAGAGAACTGCACATAATTCTGAAGCAGCTGATTTAGAAGAAAGTTTTAATGAGCATGAACTGGA
GCCTTCGTCACCTAAAAATAAAATGAAAAGTCACAAAGGAAGGCCACAAAAAAAGGGCTGTCAGAAGATACAAGGTCTAT
ATCCTCCCATGGAACAGAGGAAATGGAAGGTAGTTTGTACAGAGATAGATCTTCAAATAGAAGCAGTCCTAGTGATACAA
GGCCCAATTGTGGATTTTGTCATGTAGGGCAGGAAGAAAATGAAGCAACAGGAAAACTGCATATATTTAACACTAAGAAG
GCAGCTGCACATTATAAGTGTATGTTATTTTCTTCTGGAACAGTTCAACTCACAACATCAAGAGCAGAATTTGGAGACTT
TTGATATCAAAACTGTTCTTCAAGAGATTAAGTGAGGGTAAATAATGAAATGTACACTTTGCAGTCAGGCTGGTGCTACT
ACTGGAAGTGAAATAAAAGCCTGTGTGAAGACTTACCTTTACCACTGTGGAGTACAAGACAAAGCTAAATACATTGAAAA
TATGTCATGAGGATTTTACAAACTGTACTGTAAAAATCATAGTGGAAATGATGAGAGAGATAAAGAAGATGAAAAATGAG
AGAATAAAAGCCAGAGAAAAATAGAAATTGGTCAGCAACAACTAACTCAGCAGCAACTTAATGGAAAC
ORF - retro_ocun_1670 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.62 % |
| Parental protein coverage: | 65.48 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | YCRKHKKTAHNSEA-DLEESFNEHELEPSSPKNKKKSRKGRP-RKTNFKGLSEDTRSTSSHGTDEMESSS |
| YC.KHK.TAHNSEA.DLEESFNEHELE...P...K...K....RK...KGLSEDTRS.SSHGT.EME.S. | |
| Retrocopy | YCQKHKRTAHNSEAADLEESFNEHELE---PSSPKNKMKSHK<RKATKKGLSEDTRSISSHGTEEMEGSL |
| Parental | YRDRSPHRSSPSDTRPKCGFCHVGEEENEARGKLHIFNAKKAAAHYKCMLFSSGTVQLTTTSRAEFGD-F |
| YRDRS..RSSPSDTRP.CGFCHVG.EENEA.GKLHIFN.KKAAAHYKCMLFSSGTVQLTT.SRAEFGD.F | |
| Retrocopy | YRDRSSNRSSPSDTRPNCGFCHVGQEENEATGKLHIFNTKKAAAHYKCMLFSSGTVQLTT-SRAEFGD>F |
| Parental | DIKTVLQEIKRGKRMKCTLCSQPGATIGCEIKACVKTYHYHCGVQDKAKYIENMSRGIYKLYCKNHSGND |
| DIKTVLQEIK.G..MKCTLCSQ.GAT.G.EIKACVKTY.YHCGVQDKAKYIENMS.G.YKLYCKNHSGN. | |
| Retrocopy | DIKTVLQEIK*G*IMKCTLCSQAGATTGSEIKACVKTYLYHCGVQDKAKYIENMS*GFYKLYCKNHSGNX |
| Parental | ERDEEDEERESKSRGKIEIDQQQLTQQQLNGN |
| .................EI.QQQLTQQQLNGN | |
| Retrocopy | XXXXXXXXXXXXXXXXXEIGQQQLTQQQLNGN |
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 .11 RPM | 25 .83 RPM |
| SRP017611_kidney | 0 .10 RPM | 18 .55 RPM |
| SRP017611_liver | 0 .08 RPM | 4 .86 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1670 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1670 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1670 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000004238 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000007022 | 1 retrocopy |
retro_ocun_1670 ,
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