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 symbol: PHF6
• Ensembl ID: ENSOCUG00000007022
• Aliases: None
• Description: PHD finger protein 6 [Source:HGNC Symbol;Acc:18145]

Sequence

>retro_ocun_1670
TATTGCCAAAAACATAAGAGAACTGCACATAATTCTGAAGCAGCTGATTTAGAAGAAAGTTTTAATGAGCATGAACTGGA
GCCTTCGTCACCTAAAAATAAAATGAAAAGTCACAAAGGAAGGCCACAAAAAAAGGGCTGTCAGAAGATACAAGGTCTAT
ATCCTCCCATGGAACAGAGGAAATGGAAGGTAGTTTGTACAGAGATAGATCTTCAAATAGAAGCAGTCCTAGTGATACAA
GGCCCAATTGTGGATTTTGTCATGTAGGGCAGGAAGAAAATGAAGCAACAGGAAAACTGCATATATTTAACACTAAGAAG
GCAGCTGCACATTATAAGTGTATGTTATTTTCTTCTGGAACAGTTCAACTCACAACATCAAGAGCAGAATTTGGAGACTT
TTGATATCAAAACTGTTCTTCAAGAGATTAAGTGAGGGTAAATAATGAAATGTACACTTTGCAGTCAGGCTGGTGCTACT
ACTGGAAGTGAAATAAAAGCCTGTGTGAAGACTTACCTTTACCACTGTGGAGTACAAGACAAAGCTAAATACATTGAAAA
TATGTCATGAGGATTTTACAAACTGTACTGTAAAAATCATAGTGGAAATGATGAGAGAGATAAAGAAGATGAAAAATGAG
AGAATAAAAGCCAGAGAAAAATAGAAATTGGTCAGCAACAACTAACTCAGCAGCAACTTAATGGAAAC

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1670 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1670 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1670 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004238	1 retrocopy	retro_cjac_3034,
Oryctolagus cuniculus	ENSOCUG00000007022	1 retrocopy	retro_ocun_1670 ,