RetrogeneDB ID: retro_ocun_1423

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:81099596..81100085(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000002289
• Aliases: None
• Description: None

Sequence

>retro_ocun_1423
ATGGGCGCCACCTGGGGAAACCCCGGGTGGGTGCGGCTCGCTCTCTGCCTGGCCGGCTTGGCGCTGTCCGTCTACGCGCT
GCACGTGAAGGCGGCGCGCGCCCGGGACCGGGACTACCGCGCGCTCTGCGACGTGGGCACCGCCATCAGCTGTTCGCGCG
TCTGATCCTCCAGATGGGGTCTGGGCTTGGGGCTGGTGGAACACGTGTTGGGACAGGACAGCATCCTCAATCAATCCAAC
AGCATATTCGGCTGCATTTTCTACATACTGCAACTGGTGTTAGGCTGCCTGCGGGCACGCTGGGCCTCCATCCTGCTGAT
GCTGAGTTCCCTGGTATCCATCGCTGGTTCTGTTTACCTGGCCTGGATCCTGTTTTTCGTGCTCTATGATTTCTGCATCA
TTTGCATCACCACATACGCCATCAACATGGGCCTGATGTGGCTTAGCTTCCGGGAGGTCCCGGAACCCAAGGTCAAGGCC
AAGGGGCAC

Alignment

ORF - retro_ocun_1423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGATWGNPGWVRLALCLAGLALSVYALHVKAARARDRDYRALCDVGTAISCSRVFSSRWGRGFGLVEHVL
          MGATWGNPGWVRLALCLAGLALSVYALHVKAARARDRDYRALCDVGTAISCSRV.SSRWG.G.GLVEHVL
Retrocopy MGATWGNPGWVRLALCLAGLALSVYALHVKAARARDRDYRALCDVGTAISCSRV*SSRWGLGLGLVEHVL

Parental  GQDSILNQSNSIFGCIFYILQLVLGCLRARWASILLMLSSLVSIAGSVYLAWILFFVLYDFCIVCITTYA
          GQDSILNQSNSIFGCIFYILQLVLGCLRARWASILLMLSSLVSIAGSVYLAWILFFVLYDFCI.CITTYA
Retrocopy GQDSILNQSNSIFGCIFYILQLVLGCLRARWASILLMLSSLVSIAGSVYLAWILFFVLYDFCIICITTYA

Parental  INVGLMWLSFREVPEPKVKAKGH
          IN.GLMWLSFREVPEPKVKAKGH
Retrocopy INMGLMWLSFREVPEPKVKAKGH

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	11.64 RPM
SRP017611_kidney	0.00 RPM	19.06 RPM
SRP017611_liver	0.00 RPM	6.94 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1423 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1423 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1423 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003097	1 retrocopy	retro_cjac_4049,
Homo sapiens	ENSG00000167397	1 retrocopy	retro_hsap_4664,
Oryctolagus cuniculus	ENSOCUG00000002289	1 retrocopy	retro_ocun_1423 ,
Ochotona princeps	ENSOPRG00000016146	3 retrocopies	retro_opri_1124, retro_opri_1164, retro_opri_70,
Pongo abelii	ENSPPYG00000007306	1 retrocopy	retro_pabe_3624,
Pan troglodytes	ENSPTRG00000008031	1 retrocopy	retro_ptro_3099,