RetrogeneDB ID: retro_ocun_1741

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018838:241643..242488(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000008701
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016174
• Aliases: None
• Description: None

Sequence

>retro_ocun_1741
GGTCGGGGCTCCGGGCCGTGGCGGCGGCGCCACCTTGTGGCCGGGGCCGGAGGGGAGGCCTGGGAGGGGGCCCCGGGGGG
CGCAGGCCTGGAGTCTGAGGACCTGGAGCCTGGGGAGCTGCTGCCAGAGCCCGAGCCCGAAGAGGAGCCTCCCCGGCCCC
GCGCACCCCCGGGAATTCCGGGCCCTGGGCCTGGCTCGGGAGCCCCCGGCAACCAGGAGGAGGAGGAGGAGCCGGGACTG
GTCGAGGGTGATCCGGGGGACAGCGCCATTGAGGACCGGAGCTGGAAGCGATCAAAGCCCTAGTCAGGGAGGTGGAGGAG
GAAGCTGAGAAGCTAAAAGAGCTGCAGAACGAGGTAGAGAAGCAGATGAATATGAGTCCACCTCCAGGCAATGCTGGCCC
AGTGATCATGTCTATTGAGGAGGGGATGGAGGCTGACGCCCGTTCCATCTATGTTGGCAATGTGGACTATGGTGCAACCG
CAGAAGAGCTGGAAGCTCACTTTCATGGCTGTGGTTCAGTCAACCGTGTGAGGATACTCTGTGACAAGTTCAGTGGCCAT
CCCAAAGGGTTTGCGTATGTAGAGTTCTCAGACCAAGAGTCGGTGAGAACTTCCCTGGCCTCAGATGAGTCCCTATTTAG
AGGAAGACAAATCAAGGTGATTCCAAAACGAACCAACAGACCAGGCATCAGCACAACAGACCGGGGTTTCCCACGTGCCC
GCTACCGTGCCAGGACCACCAACTACAACAGTTCCCGCTCTAGATTCTACAGTGGTTTTAACAGCAGGCCCCGGGGTCGC
ATCTACAGGGGCCGGACTAGAGCGACATCATGGTATTCCCCTTAC

Alignment

ORF - retro_ocun_1741 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.67 %
• Parental protein coverage: 95.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRGSGPGRRRHLVPGAGGEAGEGAPGGAGDYGNGLESEELEPGELLPEPEPEEEPPRPRAPPGTPGPGPG
          GRGSGP.RRRHLV.GAG...GE...G..G..G.GLESE.LEPGELLPEPEPEEEPPRPRAPPG.PGPGPG
Retrocopy GRGSGPWRRRHLVAGAG---GEAWEGAPG--GAGLESEDLEPGELLPEPEPEEEPPRPRAPPGIPGPGPG

Parental  SGAPGNQEEEEEPGLVEGDPGDSAIED-PELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGP
          SGAPGNQEEEEEPGLVEGDPGDSAIED.PELEAIKA.VRE.EEEAEKLKELQNEVEKQMNMSPPPGNAGP
Retrocopy SGAPGNQEEEEEPGLVEGDPGDSAIED<PELEAIKALVREVEEEAEKLKELQNEVEKQMNMSPPPGNAGP

Parental  VIMSIEERMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT
          VIMSIEE.MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRV.ILCDKFSGHPKGFAY.EFSD.ESVRT
Retrocopy VIMSIEEGMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVRILCDKFSGHPKGFAYVEFSDQESVRT

Parental  SLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPRGRIYRGRAR
          SLA.DESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPRGRIYRGR.R
Retrocopy SLASDESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPRGRIYRGRTR

Parental  ATSWYSPY
          ATSWYSPY
Retrocopy ATSWYSPY

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	0.17 RPM	94.37 RPM
SRP017611_kidney	0.10 RPM	57.77 RPM
SRP017611_liver	0.08 RPM	42.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1741 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1741 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1741 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Oryctolagus cuniculus	ENSOCUG00000016174	4 retrocopies	retro_ocun_1185, retro_ocun_1741 , retro_ocun_1930, retro_ocun_365,