RetrogeneDB ID: retro_ocun_65

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 5:27705582..27706044(-)
• Located in intron of: ENSOCUG00000026433

Retrocopy information

• Ensembl ID: ENSOCUG00000021407
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016657
• Aliases: None
• Description: None

Sequence

>retro_ocun_65
ATGGCAGACGAAATTGATTTCACCACTGCAGACGCCGGGGCATCCAGCACTTACCCAGTGAAGTGCTCGGCCCTACGCAA
AAACGGCTTCGTGGTGCTGAAGGGACGACCATGCAGAATAGTGGAGATGTCAACTTCCAAAACCGGAAGGCACGGCCATG
CCAAGGTTCACCTTGTTGGAACTGATATTTTCACGGGCAAAAAATATGAAGATATTTGCCCTTCTACTCACAACATGGAT
GTTCCAAATATTAAGAGAAATGACTATCAACTGATATGCATTCAGGATGGTTACCTTTCCCTGCTGACAGAAACTGGTGA
AGTTCGTGAGGATCTTAAACTGCCAGAAGGTGAACTAGGCAAAGAAATAGAAGGCAAATACAACGCAGGCGAAGATGTCC
AGGTGTCTGTCATGTGTGCAATGAGTGAAGAATACGCTGTAGCCATAAAGCCGTGCAAATAA

Alignment

ORF - retro_ocun_65 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.08 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADEIDFTTGDAGASSTYPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYE
          MADEIDFTT.DAGASSTYP..CSALRKNGFVVLKGRPC.IVEMSTSKTG.HGHAKVHLVG.DIFTGKKYE
Retrocopy MADEIDFTTADAGASSTYPVKCSALRKNGFVVLKGRPCRIVEMSTSKTGRHGHAKVHLVGTDIFTGKKYE

Parental  DICPSTHNMDVPNIKRNDYQLICIQDGYLSLLTETGEVREDLKLPEGELGKEIEGKYNAGEDVQVSVMCA
          DICPSTHNMDVPNIKRNDYQLICIQDGYLSLLTETGEVREDLKLPEGELGKEIEGKYNAGEDVQVSVMCA
Retrocopy DICPSTHNMDVPNIKRNDYQLICIQDGYLSLLTETGEVREDLKLPEGELGKEIEGKYNAGEDVQVSVMCA

Parental  MSEEYAVAIKPCK
          MSEEYAVAIKPCK
Retrocopy MSEEYAVAIKPCK

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	3.04 RPM
SRP017611_kidney	0.00 RPM	2.03 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_65 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_65 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_65 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005363	1 retrocopy	retro_chof_1016,
Cavia porcellus	ENSCPOG00000012594	1 retrocopy	retro_cpor_1060,
Dasypus novemcinctus	ENSDNOG00000014801	2 retrocopies	retro_dnov_1133, retro_dnov_268,
Homo sapiens	ENSG00000163577	1 retrocopy	retro_hsap_1591,
Loxodonta africana	ENSLAFG00000013225	1 retrocopy	retro_lafr_901,
Macropus eugenii	ENSMEUG00000007473	2 retrocopies	retro_meug_1619, retro_meug_641,
Macaca mulatta	ENSMMUG00000022880	1 retrocopy	retro_mmul_2222,
Nomascus leucogenys	ENSNLEG00000005292	1 retrocopy	retro_nleu_1762,
Oryctolagus cuniculus	ENSOCUG00000016657	1 retrocopy	retro_ocun_65 ,
Pongo abelii	ENSPPYG00000014294	2 retrocopies	retro_pabe_1308, retro_pabe_1640,
Pan troglodytes	ENSPTRG00000015621	1 retrocopy	retro_ptro_1070,
Ictidomys tridecemlineatus	ENSSTOG00000008130	2 retrocopies	retro_itri_1400, retro_itri_689,
Tupaia belangeri	ENSTBEG00000000408	2 retrocopies	retro_tbel_1442, retro_tbel_4419,