RetrogeneDB ID: retro_ocun_1241

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:74108570..74108842(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF5
• Ensembl ID: ENSOCUG00000016417
• Aliases: None
• Description: ring finger protein 5, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:10068]

Sequence

>retro_ocun_1241
GGGGCGGGGTGGGCGTGACCTTTGAATGTACTATGTTTGGAGACTGCTCGGGAAGCTGTGGTCAGTGTGTGTGGCCACCT
GTACTGCTGGCCCTGTCTTCATCAGTGGCTGGAGACCCGGCCGGAGTGGCAGGAGTGCCCAGCATATAAGGCCAGGATCC
GCAGAGAGACTGTGTCCCACTGTATGGCGGAGGAAGCCAGAAGTCCCAGGATCCCAGATTGAAAACTCCACCTCACCCCC
AGGGCCAGCGACTGGCTCCGGAGAGCAGAGGG

Alignment

ORF - retro_ocun_1241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.52 %
• Parental protein coverage: 50.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAGATFECNI-CLETAREAVVSVCGHLYCWPCLHQWLETRPERQECPVCKAGISRETV-VPLYGRGSQKP
          GAG.....N..CLETAREAVVSVCGHLYCWPCLHQWLETRPE.QECP..KA.I.RETV.VPLYG.GSQK.
Retrocopy GAGWA*PLNVLCLETAREAVVSVCGHLYCWPCLHQWLETRPEWQECPAYKARIRRETV<VPLYGGGSQKS

Parental  QDPRLKTPPRPQGQRPAPESRG
          QDPRLKTPP.PQGQR.APESRG
Retrocopy QDPRLKTPPHPQGQRLAPESRG

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	29.36 RPM
SRP017611_kidney	0.00 RPM	41.56 RPM
SRP017611_liver	0.00 RPM	19.73 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1241 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1241 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1241 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000016417	1 retrocopy	retro_ocun_1241 ,
Otolemur garnettii	ENSOGAG00000031466	1 retrocopy	retro_ogar_1951,
Oreochromis niloticus	ENSONIG00000013523	1 retrocopy	retro_onil_48,
Ochotona princeps	ENSOPRG00000004366	2 retrocopies	retro_opri_166, retro_opri_667,
Pan troglodytes	ENSPTRG00000018010	1 retrocopy	retro_ptro_2740,
Ictidomys tridecemlineatus	ENSSTOG00000024478	1 retrocopy	retro_itri_480,
Tupaia belangeri	ENSTBEG00000016320	1 retrocopy	retro_tbel_2183,