RetrogeneDB ID: retro_ocun_1617

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018718:1246047..1246445(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023760
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000027189
• Aliases: None
• Description: None

Sequence

>retro_ocun_1617
GCCTTCTTTAGGGCAGTCGCGCAGGCAGCGGCTGCAGGAAGCCGGGCTCTGGGCGTCATGTACTACAAGTTTAGTGGCTT
CACGCAAAAGTTGACGGGAGCATGGCTTCGGACACCTATTTCCCGCAGGGATTAAAGCCTGTGGTTTCCACAGAAGCACC
ACCTATCATATTTGCTACCCCAACTAAACTGATCTCCAATTCTGCTGCATATGATTATGCTGGGAAAAACAAAGTTCCAG
AGTTGCAGAAGTTTTTCCAGAAATCTGATGGTGTGCGCATCCACCTGAAACGAGGCCTGCCTGACCAAATGCTTTACCGG
ACCACCATGGTGCTGACTGTGGGAGGGACCATCTACTGCCTGATCGCCCTCTACATGGCTTCACAGCCCAGAAACAAA

Alignment

ORF - retro_ocun_1617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.28 %
• Parental protein coverage: 91.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFFRAVAQAAAAGSRAPGVMYYKFSGFTQKLTGAW-ASDAYFPQGLKPVVSTEAPPIIFATPTKLTSNSP
          .FFRAVAQAAAAGSRA.GVMYYKFSGFTQKLTGAW.ASD.YFPQGLKPVVSTEAPPIIFATPTKL.SNS.
Retrocopy AFFRAVAQAAAAGSRALGVMYYKFSGFTQKLTGAW<ASDTYFPQGLKPVVSTEAPPIIFATPTKLISNSA

Parental  AYDYAGKNKVPELQKFFQKSDGVPIHLKRGLPDQMLYRTTMALTVGGTIYCLIALYMASQPKNK
          AYDYAGKNKVPELQKFFQKSDGV.IHLKRGLPDQMLYRTTM.LTVGGTIYCLIALYMASQP.NK
Retrocopy AYDYAGKNKVPELQKFFQKSDGVRIHLKRGLPDQMLYRTTMVLTVGGTIYCLIALYMASQPRNK

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	0.06 RPM	32.78 RPM
SRP017611_kidney	0.00 RPM	25.34 RPM
SRP017611_liver	0.00 RPM	6.71 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1617 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1617 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1617 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032040	1 retrocopy	retro_cfam_1847,
Callithrix jacchus	ENSCJAG00000014705	1 retrocopy	retro_cjac_1492,
Echinops telfairi	ENSETEG00000011940	1 retrocopy	retro_etel_650,
Homo sapiens	ENSG00000115944	1 retrocopy	retro_hsap_825,
Gorilla gorilla	ENSGGOG00000010739	1 retrocopy	retro_ggor_674,
Macaca mulatta	ENSMMUG00000016278	1 retrocopy	retro_mmul_110,
Mustela putorius furo	ENSMPUG00000008875	1 retrocopy	retro_mputfur_97,
Mus musculus	ENSMUSG00000024248	2 retrocopies	retro_mmus_32, retro_mmus_926,
Nomascus leucogenys	ENSNLEG00000016666	1 retrocopy	retro_nleu_258,
Oryctolagus cuniculus	ENSOCUG00000027189	3 retrocopies	retro_ocun_1617 , retro_ocun_1781, retro_ocun_28,
Otolemur garnettii	ENSOGAG00000016029	1 retrocopy	retro_ogar_114,
Pan troglodytes	ENSPTRG00000011865	1 retrocopy	retro_ptro_575,
Sarcophilus harrisii	ENSSHAG00000012014	1 retrocopy	retro_shar_479,
Ictidomys tridecemlineatus	ENSSTOG00000012922	1 retrocopy	retro_itri_21,
Tupaia belangeri	ENSTBEG00000014124	3 retrocopies	retro_tbel_2384, retro_tbel_4472, retro_tbel_4545,