RetrogeneDB ID: retro_ocun_461

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:3390439..3390976(-)
• Located in intron of: ENSOCUG00000015052

Retrocopy information

• Ensembl ID: ENSOCUG00000024373
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PEF1
• Ensembl ID: ENSOCUG00000005744
• Aliases: None
• Description: penta-EF-hand domain containing 1 [Source:HGNC Symbol;Acc:30009]

Sequence

>retro_ocun_461
CCTGGAACTCCAGGGGGACCATATGGTGGTGCAGCCCCAGGAAGTCCCTACTATCCACCACCTCCAAGTGCCTATGGTGC
CCAGCAGCCCGGGCCTTATGGACAGGGCGGCGCCCCTCCTGGTGTACAGCCTGAGGCCTACTCCTGGTTCTAGTCGGTGG
ACTCTGATCCCAGTGGTTTCATTTCCATCAAGGAGCTACAGCAGGCTCTGGTCAACTCCAGCTGGTCTCCGTTCAATGAT
GAGATGTGCCTCATGATGATAAACACGTTTGACAAGACCAAGTCAGGCCGCATCGATGTCTACGGGTTCTCAGCCCTGCG
GAAGTTCATCCAGCAGTGGAAGAACCTCTTCCAGCAGTATGACCGGAACCACTCGGGCTCCATCAGCTACACGGAGCTGC
AGCAAGCTCTGTCCCAGAGGGGCTACAACCTGAGCCCCCAGTTCACCCAGCTTCTGGTCTCCCACTACTGCCTGCGTTCT
GCCAGTCCCGCCATGCAGCTCGACCGTTTTATCCAGGTGTGCACTCAGCAGCAGGTG

Alignment

ORF - retro_ocun_461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.06 %
• Parental protein coverage: 61.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGTPGGPYGGAAPGSPYGPPPPSAYGAQQPGPYGQGGAPPGVDPEAYSWFQSVDSDHSGYISIKELKQAL
          PGTPGGPYGGAAPGSPY.PPPPSAYGAQQPGPYGQGGAPPGV.PEAYSWF.SVDSD.SG.ISIKEL.QAL
Retrocopy PGTPGGPYGGAAPGSPYYPPPPSAYGAQQPGPYGQGGAPPGVQPEAYSWF*SVDSDPSGFISIKELQQAL

Parental  VNSNWSSFNDETCLMMINMFDKTKSGRIDVYGFSALWKFIQQWKNLFQQYDRDHSGSISYTELQQALSQM
          VNS.WS.FNDE.CLMMIN.FDKTKSGRIDVYGFSAL.KFIQQWKNLFQQYDR.HSGSISYTELQQALSQ.
Retrocopy VNSSWSPFNDEMCLMMINTFDKTKSGRIDVYGFSALRKFIQQWKNLFQQYDRNHSGSISYTELQQALSQR

Parental  GYNLSPQFTQLLVSRYCPRSASPAMQLDRFIQVCTQLQV
          GYNLSPQFTQLLVS.YC.RSASPAMQLDRFIQVCTQ.QV
Retrocopy GYNLSPQFTQLLVSHYCLRSASPAMQLDRFIQVCTQQQV

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	0.06 RPM	37.03 RPM
SRP017611_kidney	0.00 RPM	32.23 RPM
SRP017611_liver	0.00 RPM	11.87 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_461 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_461 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_461 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006355	1 retrocopy	retro_cjac_1745,
Homo sapiens	ENSG00000162517	1 retrocopy	retro_hsap_497,
Gorilla gorilla	ENSGGOG00000015897	1 retrocopy	retro_ggor_464,
Macropus eugenii	ENSMEUG00000014458	1 retrocopy	retro_meug_375,
Microcebus murinus	ENSMICG00000001374	1 retrocopy	retro_mmur_937,
Macaca mulatta	ENSMMUG00000023397	1 retrocopy	retro_mmul_146,
Monodelphis domestica	ENSMODG00000017573	1 retrocopy	retro_mdom_1930,
Nomascus leucogenys	ENSNLEG00000001979	1 retrocopy	retro_nleu_2422,
Oryctolagus cuniculus	ENSOCUG00000002868	2 retrocopies	retro_ocun_1786, retro_ocun_741,
Oryctolagus cuniculus	ENSOCUG00000005744	1 retrocopy	retro_ocun_461 ,
Pongo abelii	ENSPPYG00000001611	1 retrocopy	retro_pabe_238,
Pan troglodytes	ENSPTRG00000000463	1 retrocopy	retro_ptro_375,
Rattus norvegicus	ENSRNOG00000013972	2 retrocopies	retro_rnor_1563, retro_rnor_2505,