RetrogeneDB ID: retro_ocun_481

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:58553620..58554277(-)
• Located in intron of: ENSOCUG00000006883

Retrocopy information

• Ensembl ID: ENSOCUG00000000065
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000008945
• Aliases: None
• Description: None

Sequence

>retro_ocun_481
GTGATCCAGGCGGAGGAGGTGACCGAGACCGAGGAAATGGCGGCAGCCGGGCTCAGCGTGACCGTCACCCACAGCAATGA
GAAGCATGACCTTCATGTCACCCCTCAGCAGGGTAGCAGCGAACCAATTGTCCAAGACCTGGCCCAGGTTGTTGAAGAGG
CCATAAGGGTTCCACTGCCTTTCCAGAAACTCATATTTAAGGAAAAATCTCTGAAGGAAATGGAGGCACCATTGTCAGCA
CTTGGAATACAAAACGGTTGCCGGGTCATGTTAATTGGGGAAAAGAACTGTCCAGAGGAAGAGGCTGAACTAAAGAAGTT
GAAGGATTTGGAGAAGTCTGTGGAGAAGATAGCCAGCCAACTAGAAGAGTTGAATAAAGAACTCAGTGGAATCCAACAGG
GTTTTCTGGCCAAGGATTTGCAAGCTGAAGCTCTCAGCAAACTTGATAGGAGAGTAAAAGCCACAATTGAGCATTTTATG
AAGATTTTGGAGGAGATTGACACCCTGATCCTACCAGAAAATTTCAAAGACAGTAGACTGAAAAGGAAGGGTTTGGTGAA
GAAGATCCAGGCGTTCCTAGCTGAGTGCGACACAGTGGAGCAGAACATCTGCCAGGAGACTGAGAGGCTCCAGTCTACAA
ACTTGGCCTTGGCTGAG

Alignment

ORF - retro_ocun_481 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.17 %
• Parental protein coverage: 65.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VIQAEEVTETEEMAAAGLSVTVTHSNEKHDLHVTPQQGSSEPIVQDLAQVVEEAIGVPLPFQKLIFKGKS
          VIQAEEVTETEEMAAAGLSVTVTHSNEKHDLHVTPQQGSSEPIVQDLAQVVEEAI.VPLPFQKLIFK.KS
Retrocopy VIQAEEVTETEEMAAAGLSVTVTHSNEKHDLHVTPQQGSSEPIVQDLAQVVEEAIRVPLPFQKLIFKEKS

Parental  LKEMETPLSALGIQNGCRVMLIGEKNCPEEEVELKKLKDLEKSVEKIASQLEELNKELSGIQQGFLAKDL
          LKEME.PLSALGIQNGCRVMLIGEKNCPEEE.ELKKLKDLEKSVEKIASQLEELNKELSGIQQGFLAKDL
Retrocopy LKEMEAPLSALGIQNGCRVMLIGEKNCPEEEAELKKLKDLEKSVEKIASQLEELNKELSGIQQGFLAKDL

Parental  QAEALSKLDRRVKATIEHFMKILEEIDTLILPENFKDSRLKRKGLVKKIQAFLAECDTVEQNICQETERL
          QAEALSKLDRRVKATIEHFMKILEEIDTLILPENFKDSRLKRKGLVKKIQAFLAECDTVEQNICQETERL
Retrocopy QAEALSKLDRRVKATIEHFMKILEEIDTLILPENFKDSRLKRKGLVKKIQAFLAECDTVEQNICQETERL

Parental  QSTNLALAE
          QSTNLALAE
Retrocopy QSTNLALAE

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	0.28 RPM	45.31 RPM
SRP017611_kidney	0.61 RPM	61.02 RPM
SRP017611_liver	0.15 RPM	11.33 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_481 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_481 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_481 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017845	1 retrocopy	retro_btau_901,
Choloepus hoffmanni	ENSCHOG00000012656	1 retrocopy	retro_chof_2328,
Callithrix jacchus	ENSCJAG00000008074	1 retrocopy	retro_cjac_4052,
Equus caballus	ENSECAG00000017942	1 retrocopy	retro_ecab_267,
Homo sapiens	ENSG00000107262	1 retrocopy	retro_hsap_4673,
Gorilla gorilla	ENSGGOG00000016534	1 retrocopy	retro_ggor_2899,
Macaca mulatta	ENSMMUG00000020148	1 retrocopy	retro_mmul_2487,
Nomascus leucogenys	ENSNLEG00000005204	1 retrocopy	retro_nleu_2165,
Oryctolagus cuniculus	ENSOCUG00000008945	1 retrocopy	retro_ocun_481 ,
Pongo abelii	ENSPPYG00000019138	1 retrocopy	retro_pabe_3630,
Pan troglodytes	ENSPTRG00000020856	1 retrocopy	retro_ptro_3105,
Tursiops truncatus	ENSTTRG00000010573	2 retrocopies	retro_ttru_252, retro_ttru_946,