RetrogeneDB ID: retro_ocun_943

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:41093225..41093917(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021392
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016138
• Aliases: None
• Description: GrpE protein homolog [Source:UniProtKB/TrEMBL;Acc:G1TAZ2]

Sequence

>retro_ocun_943
TCCTCCTGGATTGCGAACATGGCCGCGCGGTCGCTGTGGGCGGTCCGGCGGCGGGTGCAGCGCCTGCTGACCTCGAGTGC
TGCGCGGGAGAACAGAGGATGGCTGCCGCCATTCAGCACTGCCACCCAGAGAACTGCTGGTGAGGACTGCAGTTCCGAGG
ACCCTCCAGATGAGCTTGGGCCATCTCTTACTGAACGAGCCCTAAGGCTAAAAGCTGTGAAACTGGAAAAGGAAGTCCAG
GATTTAACAATAAGATACCAGAGAGCTGTGGCTGACTGTGAAAATATAAGGAGGCGGACCCAGAGATGTGTGAAGATGCC
AAGATATTTGGAATCCAGAGTTTCTGTAAGGACTTGGTGGAGATGGCGGACATTTTGGAGAAGACTACTGAGTGCATTTC
TGAAGAAACAGAGTCTGGGGACCAGACACTCATTCTGGAGAAGGTCTTTCGGGGGCTGTCACTCCTAGAAGCAAAGCTGA
AAAGTGTGTTTGCCAAGCATGGCCTGGAGAAGATGGCACCCATCGGTGATAAATACGACCCTCATGAGCATGAACTCATC
TGTCACGTGCCAGCTGGCGTTGGGGTGCAGCCTGGCACGGTGGCATTAGTAAGACAAGATGGCTACAAACTTCATGGTCG
CACCATTAGACTTGCCCAGGTAGAAGTGGCAGTGGAGTCTCAGAGAAGACTA

Alignment

ORF - retro_ocun_943 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.71 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSWIANMAARSLWAVRRRVQRLLTSSAAWENRGWLPPFSTATQRTAGEDCSSEDPPDELGPSLTERALRL
          SSWIANMAARSLWAVRRRVQRLLTSSAA.ENRGWLPPFSTATQRTAGEDCSSEDPPDELGPSLTERALRL
Retrocopy SSWIANMAARSLWAVRRRVQRLLTSSAARENRGWLPPFSTATQRTAGEDCSSEDPPDELGPSLTERALRL

Parental  KAVKLEKEVQDLTIRYQRAVADCENIRRRTQRCV-EDAKIFGIQSFCKDLVEVADILEKTTECISEETES
          KAVKLEKEVQDLTIRYQRAVADCENIRRRTQRCV.EDAKIFGIQSFCKDLVE.ADILEKTTECISEETES
Retrocopy KAVKLEKEVQDLTIRYQRAVADCENIRRRTQRCV<EDAKIFGIQSFCKDLVEMADILEKTTECISEETES

Parental  GDQTLILEKVFRGLSLLEAKLKSVFAKHGLEKMAPIGDKYDPHEHELICHVPAGVGVQPGTVALVRQDGY
          GDQTLILEKVFRGLSLLEAKLKSVFAKHGLEKMAPIGDKYDPHEHELICHVPAGVGVQPGTVALVRQDGY
Retrocopy GDQTLILEKVFRGLSLLEAKLKSVFAKHGLEKMAPIGDKYDPHEHELICHVPAGVGVQPGTVALVRQDGY

Parental  KLHGRTIRLAQVEVAVESQRRL
          KLHGRTIRLAQVEVAVESQRRL
Retrocopy KLHGRTIRLAQVEVAVESQRRL

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	0.72 RPM	5.24 RPM
SRP017611_kidney	0.41 RPM	3.55 RPM
SRP017611_liver	0.31 RPM	0.92 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_943 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_943 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_943 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004070	1 retrocopy	retro_chof_1984,
Dipodomys ordii	ENSDORG00000011142	1 retrocopy	retro_dord_353,
Felis catus	ENSFCAG00000003624	1 retrocopy	retro_fcat_618,
Homo sapiens	ENSG00000164284	2 retrocopies	retro_hsap_1284, retro_hsap_4842,
Gorilla gorilla	ENSGGOG00000005410	2 retrocopies	retro_ggor_1008, retro_ggor_3021,
Macaca mulatta	ENSMMUG00000021662	1 retrocopy	retro_mmul_1317,
Nomascus leucogenys	ENSNLEG00000010160	1 retrocopy	retro_nleu_710,
Oryctolagus cuniculus	ENSOCUG00000016138	3 retrocopies	retro_ocun_89, retro_ocun_905, retro_ocun_943 ,
Otolemur garnettii	ENSOGAG00000014326	1 retrocopy	retro_ogar_791,
Pongo abelii	ENSPPYG00000015933	2 retrocopies	retro_pabe_1063, retro_pabe_3764,
Pan troglodytes	ENSPTRG00000017396	2 retrocopies	retro_ptro_3226, retro_ptro_877,
Sorex araneus	ENSSARG00000005467	2 retrocopies	retro_sara_320, retro_sara_511,