RetrogeneDB ID: retro_ocun_905

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:17021465..17022044(+)
• Located in intron of: ENSOCUG00000011752

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ocun_905
TCCTCCTGAATGGCAAACATGACCATGGAGTCGCTATGGGTTGTCTGGCAGCTGGTGTGGCACCTCCTGGCCTCAGATAC
TATGTAGGAGAACAGAAGATGGCTGCACCCATTCAGCACAGTTACCCAACAAACAGCTGGTGAAGACTGCAGTTCTGAGG
ACCCTCCTGGTGAGCTTGGGCCCTTTCTTACTGAATGAGCCTTACTGCTAAAAGCTGTGAAATTGGATATAGAAGTCCAG
TATTTAACTATAAGATATCAGAGAGCTGTGGCTGATTGTGAAAACATAAGGAGGTGGACCAAAAGATGTGTGGAAGATGC
CAAGATATTTGGAATCCAGAGTTTCTGTAAGGACTTGATGGAGATGGCAGACATTTTGGAGAAGACTTCTAAGTGTGTTT
CTGAAGATACAAAGCCTGGAGACCAGACACTTAACTGTGGAGAAGGTCTTCTGGCGTTGTTACTACCAGAAGCAAAGCTG
AAAAATCTGTTTACTGAGCATGACATGGAGAAGATAGTACCTATTTGTGATAAATATGACCCTCATGAGCATGAACTCAT
CTGTCACGTGCCAGCTGGT

Alignment

ORF - retro_ocun_905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.98 %
• Parental protein coverage: 83.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSWIANMAARSLWAVRRRVQRLLTSSAAWENRGWLPPFSTATQRTAGEDCSSEDPPDELGPSLTERALRL
          SS..ANM...SLW.V...V..LL.S....ENR.WL.PFST.TQ.TAGEDCSSEDPP.ELGP.LTE.AL.L
Retrocopy SS*MANMTMESLWVVWQLVWHLLASDTM*ENRRWLHPFSTVTQQTAGEDCSSEDPPGELGPFLTE*ALLL

Parental  KAVKLEKEVQDLTIRYQRAVADCENIRRRTQRCVEDAKIFGIQSFCKDLVEVADILEKTTECISEETESG
          KAVKL..EVQ.LTIRYQRAVADCENIRR.T.RCVEDAKIFGIQSFCKDL.E.ADILEKT..C.SE.T..G
Retrocopy KAVKLDIEVQYLTIRYQRAVADCENIRRWTKRCVEDAKIFGIQSFCKDLMEMADILEKTSKCVSEDTKPG

Parental  DQTLILEKVFRGLSLLEAKLKSVFAKHGLEKMAPIGDKYDPHEHELICHVPAG
          DQTL........L.L.EAKLK..F..H..EK..PI.DKYDPHEHELICHVPAG
Retrocopy DQTLNCGEGLLALLLPEAKLKNLFTEHDMEKIVPICDKYDPHEHELICHVPAG

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	5.24 RPM
SRP017611_kidney	0.00 RPM	3.55 RPM
SRP017611_liver	0.00 RPM	0.92 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_905 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_905 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_905 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,