RetrogeneDB ID: retro_ocun_20

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:55513231..55513684(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000016851
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000025904
• Aliases: None
• Description: None

Sequence

>retro_ocun_20
ATGGACGCGGACGTTGGAGCTGCTGAGGCCCGGCAGGACCCATTGAAGCCGGCCCGCCCAGAGGACCTGCTTAAGTTCCC
ACATCCACCGCCGCCCCCGCGCATTCACATCCGGCCGTGGTGGTTTCCGGAGCAGGAACTGGAAGACCCCTTGGTGTTCC
ACCTGGAGGCATGGGTGGCAGACATGATCTTTGGCCCAGACCGAGCCAGGATTCCGGAAATGGAGTGGATGAGCCAGGCC
CTGTTGAGGGTGGACAGAGTGGACTTCAGGAATTTAGTGGAAAGCACGGTCCACGGACGGCCCCGTGTGCGGAACCGGGT
GAAGAGCATTCTCCTGAGCCTGGCGTCATGGCACCGAGAACGTCGTGCGCGGCGAGCCGAGAAGATGAAGCACCTTGAGG
AGTTCCTGAAGACGCGTTCATGGGGCCAGACGCTCCCCTGCATCTCGAAACTT

Alignment

ORF - retro_ocun_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.25 %
• Parental protein coverage: 96.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTDVGAAEARQHPLKLTRPEDLLRFPHPLPPPRIHIRPWWFPVQELEDPAVFYLEAWVADLIFGPDRAM
          MD.DVGAAEARQ.PLK..RPEDLL.FPHP.PPPRIHIRPWWFP.QELEDP.VF.LEAWVAD.IFGPDRA.
Retrocopy MDADVGAAEARQDPLKPARPEDLLKFPHPPPPPRIHIRPWWFPEQELEDPLVFHLEAWVADMIFGPDRAR

Parental  IPEMEWMSQALLRVDPVDSGNLVEITVHARPRVQNRVKSILLSLASWHRERRVARAEKMKHLEEFLKTRS
          IPEMEWMSQALLRVD.VD..NLVE.TVH.RPRV.NRVKSILLSLASWHRERR..RAEKMKHLEEFLKTRS
Retrocopy IPEMEWMSQALLRVDRVDFRNLVESTVHGRPRVRNRVKSILLSLASWHRERRARRAEKMKHLEEFLKTRS

Parental  SGPDAP
          .G...P
Retrocopy WGQTLP

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_20 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_20 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_20 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009962	1 retrocopy	retro_cjac_3033,
Homo sapiens	ENSG00000203907	3 retrocopies	retro_hsap_432, retro_hsap_4807, retro_hsap_543,
Gorilla gorilla	ENSGGOG00000016832	3 retrocopies	retro_ggor_2992, retro_ggor_422, retro_ggor_495,
Loxodonta africana	ENSLAFG00000012754	2 retrocopies	retro_lafr_412, retro_lafr_782,
Myotis lucifugus	ENSMLUG00000017174	2 retrocopies	retro_mluc_115, retro_mluc_252,
Macaca mulatta	ENSMMUG00000000416	2 retrocopies	retro_mmul_2561, retro_mmul_519,
Nomascus leucogenys	ENSNLEG00000001204	2 retrocopies	retro_nleu_2182, retro_nleu_717,
Oryctolagus cuniculus	ENSOCUG00000025904	1 retrocopy	retro_ocun_20 ,
Pan troglodytes	ENSPTRG00000029545	3 retrocopies	retro_ptro_3197, retro_ptro_329, retro_ptro_408,
Rattus norvegicus	ENSRNOG00000025957	1 retrocopy	retro_rnor_2192,
Tursiops truncatus	ENSTTRG00000001487	2 retrocopies	retro_ttru_1376, retro_ttru_1803,