RetrogeneDB ID: retro_ocun_1193

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:61876621..61877268(-)
• Located in intron of: ENSOCUG00000001687

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5B
• Ensembl ID: ENSOCUG00000013895
• Aliases: None
• Description: RAB5B, member RAS oncogene family [Source:HGNC Symbol;Acc:9784]

Sequence

>retro_ocun_1193
TTGTCACTTTGTGGCAGAAGCATAGCCAGGCCCAATGGGCAGCCTAAGGCCACCAATATATGCCAATGCAAACTGGTCTT
GCAGGACAATCTGCAATGCAAAAATCTATTCTGGTATTTTGTTTTGTCAAAGGACAATTTCATGAGTACCAGGAGAGTAC
CACTGGAGCAATCTTCCTCACCAACTCTGTTTGTCTGGACATGACAACAGTCAAGTCTGAGATCTGGGTCACAGTTGGAA
GGGAGTGATACCACAGCTTAGTCTGCATGTACTACAGAGATGTCCAAGCTGAAATCATGGTTTATGAAATTACTAATCAG
GAAACATTTGCCCAAGCAAAGACATGGGTAAAGGAATTACAGAGGCAGGCCAGTCTTAGCATCATAATTGCCCTGGTGGG
GAACAAAGCTGACCTGACTGAAAAGTGCACGATCGAATATGAAGAGGCTTGAGGACATGCAGATGACAACAGCTTACTGT
TTATAGAGACTCTAGCCAAGACGTCTATGAACATGTATGATTTCTTTCTGGCAATAGCTAAGAAGTTGCTAAAGAGTGAA
CCCTAGAATCTGGGGGCTGCAGCAGGCCAAAGCTGTGGTATAGACCTCCATGAGCAGTCCCAGCAGAACAAAAATCAGTG
TTGTAGC

Alignment

ORF - retro_ocun_1193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.27 %
• Parental protein coverage: 95.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAMTSRSTARPNGQPQASKICQFKLVL-LGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQSVCLDDT
          L....RS.ARPNGQP.A..ICQ.KLVL..G.SA..KS.LV..FVKGQFHEYQEST.GA.FLT.SVCLD.T
Retrocopy LSLCGRSIARPNGQPKATNICQCKLVL<AGQSAMQKSILVFCFVKGQFHEYQESTTGAIFLTNSVCLDMT

Parental  TVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADL
          TVK.EIW.T.G.E.YHSL..MYYR..QA.I.VY.ITNQETFA.AKTWVKELQRQAS.SI.IAL.GNKADL
Retrocopy TVKSEIWVTVGRE*YHSLVCMYYRDVQAEIMVYEITNQETFAQAKTWVKELQRQASLSIIIALVGNKADL

Parental  ANKRMVEYEEAQAYADDNSLLFMETSAKTAMNVNDLFLAIAKKLPKSEPQNLGGAAGRSRGVDLHEQSQQ
          ..K...EYEEA...ADDNSLLF.ET.AKT.MN..D.FLAIAKKL.KSEP.NLG.AAG.S.G.DLHEQSQQ
Retrocopy TEKCTIEYEEA*GHADDNSLLFIETLAKTSMNMYDFFLAIAKKLLKSEP*NLGAAAGQSCGIDLHEQSQQ

Parental  NKSQCCS
          NK.QCCS
Retrocopy NKNQCCS

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	0.00 RPM	37.97 RPM
SRP017611_kidney	0.00 RPM	38.41 RPM
SRP017611_liver	0.00 RPM	20.35 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1193 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1193 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007527	2 retrocopies	retro_cjac_1215, retro_cjac_1879,
Dasypus novemcinctus	ENSDNOG00000016952	1 retrocopy	retro_dnov_350,
Equus caballus	ENSECAG00000023306	1 retrocopy	retro_ecab_280,
Echinops telfairi	ENSETEG00000009603	2 retrocopies	retro_etel_617, retro_etel_698,
Mus musculus	ENSMUSG00000000711	1 retrocopy	retro_mmus_2081,
Nomascus leucogenys	ENSNLEG00000017570	1 retrocopy	retro_nleu_2531,
Oryctolagus cuniculus	ENSOCUG00000004414	1 retrocopy	retro_ocun_554,
Oryctolagus cuniculus	ENSOCUG00000012200	1 retrocopy	retro_ocun_1034,
Oryctolagus cuniculus	ENSOCUG00000013895	1 retrocopy	retro_ocun_1193 ,
Ochotona princeps	ENSOPRG00000007883	3 retrocopies	retro_opri_1061, retro_opri_1116, retro_opri_299,
Procavia capensis	ENSPCAG00000010486	1 retrocopy	retro_pcap_380,