RetrogeneDB ID: retro_ocun_28

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:32463536..32463881(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022605
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_ocun_28
ATGTACTACAAGTTTAGTGGCTTCACGCAAAAGTTGACGGGAGCATGGGCTTCAGATGCCTATTTCCCACAGGGATTAAA
GCCTGTGGTTTCCACAGAGGCACCACCTATCATATTTGCTACTCCAACTAAATTGACCTCCAACTCTCCCGCATATGATT
ATGCTGGGAAAAACAAAGTTCCAGAGTTGCAGAAGTTTTTCCAGAAATCTGATGGTGTACCCATCCACCTGAAACGAGGC
CTGCCTAACCAAACGCTTTACCTGACCACCATGGCGCTGACTGTGGGAGGGACCATCTACTGCCTTATGGCCCTCTACAT
GGCTTCACAGCCCAAAAGCAGATGA

Alignment

ORF - retro_ocun_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 78.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYYKFSGFTQKLTGAWASDAYFPQGLKPVVSTEAPPIIFATPTKLTSNSPAYDYAGKNKVPELQKFFQKS
          MYYKFSGFTQKLTGAWASDAYFPQGLKPVVSTEAPPIIFATPTKLTSNSPAYDYAGKNKVPELQKFFQKS
Retrocopy MYYKFSGFTQKLTGAWASDAYFPQGLKPVVSTEAPPIIFATPTKLTSNSPAYDYAGKNKVPELQKFFQKS

Parental  DGVPIHLKRGLPDQMLYRTTMALTVGGTIYCLIALYMASQPKNK
          DGVPIHLKRGLP.Q.LY.TTMALTVGGTIYCL.ALYMASQPK..
Retrocopy DGVPIHLKRGLPNQTLYLTTMALTVGGTIYCLMALYMASQPKSR

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	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_28 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_28 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_28 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,