RetrogeneDB ID: retro_ocun_361

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:49462515..49463292(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000013279
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000002085
• Aliases: None
• Description: None

Sequence

>retro_ocun_361
GGCCGGAGCCAGTGTCAACCAGTGTCACCTGGACCTCTCCATTGCCTAAAGGTGATCTTGGAAAAAGAAGGGCCTCGTTT
CCTATTTAGAGGATTAGGCCCCAATTTAGTGGGGGTAGCCCCTTCCAGAGCAATATACTTTGCTGCTTATTCAAACTGCA
AGGAAAAGTTGAGTGGTGTATTTGATCCTCATTCTACCCAGGTACACATGATTTCAGCTGCAATGGCAGGTTTTACTGCA
ATCACAGCAACTAACCCCATCTGGCTTATAACGACTCGGTTACAACTTGATGCAAGGAGCCGTGGGGAAAAGCGATTGGG
TGCTTTTGAATGTGTTCGCAAAGTATATCAGACAGATGGACTTAGAGGATTTTACAGGGGCATGTCTGCTTCCTATGCTG
GCATATCAGAGACTGTTATCCACTTTGTTATTTATGAAAGTATAAAGCAAAAACTGCTGGAATGTAAGACTGCCTCTATG
ATGGAAAACGATGAAGAGTCTGTGAAGGAAGCATCAGATTTTGTGGGAATGATGCTGGCTGCAGCCACCTCAAAGACTTG
TGCCACAACTATCGCATACCCTCATGAAGTTGTAAGAACAAGACTACGTGAAGAGGGAACAAAATATAGATCATTTTTTC
AGACACTCTCTTTGGTTGTTCAAGAAGAAGGTTATGGATCTCCTTACCGTGGCCTAACAACTCATCTGGTGAGACAGATT
CCAAACACAGCCATTATGATAGCCACCTATGAATTGGTGGTGTACCTACTCAATGGA

Alignment

ORF - retro_ocun_361 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.75 %
• Parental protein coverage: 83.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GASVNRIVSPGPLHCLKVILEKEGPRSLFRGLGPNLVGVAPSRAIYFAAYSNCKEKLNGVFDPDSTQVHM
          G.S....VSPGPLHCLKVILEKEGPR.LFRGLGPNLVGVAPSRAIYFAAYSNCKEKL.GVFDP.STQVHM
Retrocopy GRSQCQPVSPGPLHCLKVILEKEGPRFLFRGLGPNLVGVAPSRAIYFAAYSNCKEKLSGVFDPHSTQVHM

Parental  ISAAMAGFTAITATNPIWLIKTRLQLDARSRGEKRLGAFECVRKVYQTDGLRGFYRGMSASYAGISETVI
          ISAAMAGFTAITATNPIWLI.TRLQLDARSRGEKRLGAFECVRKVYQTDGLRGFYRGMSASYAGISETVI
Retrocopy ISAAMAGFTAITATNPIWLITTRLQLDARSRGEKRLGAFECVRKVYQTDGLRGFYRGMSASYAGISETVI

Parental  HFVIYESIKQKLLECKTASMMENDEESVKEASDFVGMMLAAATSKTCATTIAYPHEVVRTRLREEGTKYR
          HFVIYESIKQKLLECKTASMMENDEESVKEASDFVGMMLAAATSKTCATTIAYPHEVVRTRLREEGTKYR
Retrocopy HFVIYESIKQKLLECKTASMMENDEESVKEASDFVGMMLAAATSKTCATTIAYPHEVVRTRLREEGTKYR

Parental  SFFQTLSLVVQEEGYGSLYRGLTTHLVRQIPNTAIMMATYELVVYLLNG
          SFFQTLSLVVQEEGYGS.YRGLTTHLVRQIPNTAIM.ATYELVVYLLNG
Retrocopy SFFQTLSLVVQEEGYGSPYRGLTTHLVRQIPNTAIMIATYELVVYLLNG

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	0.22 RPM	8.22 RPM
SRP017611_kidney	0.10 RPM	12.06 RPM
SRP017611_liver	0.00 RPM	0.46 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_361 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_361 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_361 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010094	1 retrocopy	retro_ecab_234,
Felis catus	ENSFCAG00000027489	1 retrocopy	retro_fcat_1680,
Macaca mulatta	ENSMMUG00000022153	1 retrocopy	retro_mmul_2243,
Mus musculus	ENSMUSG00000032449	1 retrocopy	retro_mmus_2007,
Oryctolagus cuniculus	ENSOCUG00000002085	1 retrocopy	retro_ocun_361 ,
Pteropus vampyrus	ENSPVAG00000007958	1 retrocopy	retro_pvam_719,
Sus scrofa	ENSSSCG00000011669	1 retrocopy	retro_sscr_871,
Tupaia belangeri	ENSTBEG00000001759	1 retrocopy	retro_tbel_3349,
Tursiops truncatus	ENSTTRG00000003288	2 retrocopies	retro_ttru_1146, retro_ttru_947,
Vicugna pacos	ENSVPAG00000008292	1 retrocopy	retro_vpac_603,