RetrogeneDB ID: retro_ocun_1200

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:86607599..86608151(-)
• Located in intron of: ENSOCUG00000008230

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSOCUG00000029552
• Aliases: None
• Description: RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]

Sequence

>retro_ocun_1200
ATGAGTGAATATAAACTAGTTGTTCTTGCTCAGGAAGTGTTGGAAAGTCTGCTCTGACTGTACATTTTGTTCAAGGAATT
TTTGTTGAAAAATATGATCCTATGATAGAAGATTCTTACAGAAAGCAAATTGAAGTAGATGCCCAACAGTATATGCTTGA
AATTTTGGGTAATGCAAGAATGGAACAATTTATAGCAATGGGAGATTTGTACATGAAACATGGACAAGGCTTTTCATTAG
TTTATTCCATCACAGCACAGTCCACATTTAACGATTTACATGATCTGAAAACACAGAATCTTTGAGTTAAAAGACACTGA
TGATGTTACAATGATTCTGGTTGGTAATAACTGGGATTTGGAAGATAAAAGAGTTGTAGGAAATGAACAAGGTCAAAATC
TAGCAAGACAATGGAACATCTGTGCATTCTTAGAATCTTCTGCAAAATCAAAAATAAATGTTAATGAGATTTTTTATGAC
ATAGTGTGGCAAATTAACAGAAAAACTCCAGTGCTTGGGAAGGCCCACAAAAAGTCATCATGTCATCTGCTT

Alignment

ORF - retro_ocun_1200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.72 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLG-SGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRD
          M.EYKLVVL..SG.VGKSALTV.FVQGIFVEKYDP.IEDSYRKQ.EVDAQQ.MLEIL..A..EQF.AM.D
Retrocopy MSEYKLVVLA<SGSVGKSALTVHFVQGIFVEKYDPMIEDSYRKQIEVDAQQYMLEILGNARMEQFIAMGD

Parental  LYMKNGQGFALVYSITAQSTFNDLQDLREQ-ILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQW
          LYMK.GQGF.LVYSITAQSTFNDL.DL..Q.I...KDTDDV.MILVGN..DLED.RVVG.EQGQNLARQW
Retrocopy LYMKHGQGFSLVYSITAQSTFNDLHDLKTQ>IFELKDTDDVTMILVGNNWDLEDKRVVGNEQGQNLARQW

Parental  NNCAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
          N.CAFLESSAKSKINVNEIFYD.V.QINRKTPV.GKA.KKSSC.LL
Retrocopy NICAFLESSAKSKINVNEIFYDIVWQINRKTPVLGKAHKKSSCHLL

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	47.19 RPM
SRP017611_kidney	0.00 RPM	67.71 RPM
SRP017611_liver	0.00 RPM	20.81 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1200 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1200 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dasypus novemcinctus	ENSDNOG00000019724	18 retrocopies	retro_dnov_1243, retro_dnov_1249, retro_dnov_1323, retro_dnov_1395, retro_dnov_1574, retro_dnov_1710, retro_dnov_1763, retro_dnov_1841, retro_dnov_186, retro_dnov_1976, retro_dnov_2033, retro_dnov_217, retro_dnov_2679, retro_dnov_298, retro_dnov_318, retro_dnov_719, retro_dnov_761, retro_dnov_84,
Erinaceus europaeus	ENSEEUG00000010052	1 retrocopy	retro_eeur_327,
Echinops telfairi	ENSETEG00000000242	1 retrocopy	retro_etel_11,
Gorilla gorilla	ENSGGOG00000025649	1 retrocopy	retro_ggor_2836,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Microcebus murinus	ENSMICG00000013148	1 retrocopy	retro_mmur_116,
Macaca mulatta	ENSMMUG00000011442	2 retrocopies	retro_mmul_1151, retro_mmul_1863,
Oryctolagus cuniculus	ENSOCUG00000022455	1 retrocopy	retro_ocun_850,
Oryctolagus cuniculus	ENSOCUG00000029552	5 retrocopies	retro_ocun_1132, retro_ocun_1200 , retro_ocun_597, retro_ocun_636, retro_ocun_796,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403,
Pan troglodytes	ENSPTRG00000005197	3 retrocopies	retro_ptro_1812, retro_ptro_2383, retro_ptro_2877,
Rattus norvegicus	ENSRNOG00000007048	4 retrocopies	retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872,
Sus scrofa	ENSSSCG00000021148	1 retrocopy	retro_sscr_1125,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,