RetrogeneDB ID: retro_ocun_862

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:29624523..29625132(+)
• Located in intron of: ENSOCUG00000009346

Retrocopy information

• Ensembl ID: ENSOCUG00000024765
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUDT5
• Ensembl ID: ENSOCUG00000009308
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 5 [Source:HGNC Symbol;Acc:8052]

Sequence

>retro_ocun_862
ATGGAAAATCAAGAAGCAACAGATTCTACTCAGAATGCCAAACAGTGTATTATTTTAGAGGAGTTAATTTCAGAAGGAAA
ATGGGTCAAGCTTGAAAAAACAACTTACACGGATCCTACTGGTAAAACTCGAACCTGGGAAACAGTGAAACGTACAACCA
AAAAGGCACAGTACGCTGATGGTGTAGCGGTCATTCCGGTGCTGCAAAGAACTCTTCACTATGAGTGTATAGTTCTGGTG
AAACAGTTCCAGCCGCCAATGGGAGGCTACTGTCTCGAGTTCCCGGTAGGTCTCATGGACGACGGTGAAAGCCCAGAAGC
AGCTGCGCTCCGGGAGCTGGAGGAGGAGATGGGCTACAAAGGTGACATTGCTGAGTGCTCTCCAGCTGTATGTATGGATC
CAGGCTTGTCCAACTGCACCACCCACATAGTGACAGTAACGATTAATGGAGATGACGCCGAGAACGTCAGACCAAAGCCA
AAGCCAGGAGGAGAATTTGTGGAAGTCATTTCTTTACCAAAGAACGACCTGCTCAAAAGACTTGATGCTCTGATAGCCAA
AGAACATCTCACAGTGGATGCCAGGGTCTATTCCTATGCTCTGGCACTG

Alignment

ORF - retro_ocun_862 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.1 %
• Parental protein coverage: 93.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MENQEATDSTQNVKQCIISEELISEGKWVKLEKTTYLDPTGKTRTWETVKRTTKKAQSADGVAVIPVLQR
          MENQEATDSTQN.KQCII.EELISEGKWVKLEKTTY.DPTGKTRTWETVKRTTKKAQ.ADGVAVIPVLQR
Retrocopy MENQEATDSTQNAKQCIILEELISEGKWVKLEKTTYTDPTGKTRTWETVKRTTKKAQYADGVAVIPVLQR

Parental  TLHYECIVLVKQFRPPMGGYCLEFPAGLIDDGESPEAAALRELEEETGYKGDIAECSPAVCMDPGLSNCT
          TLHYECIVLVKQF.PPMGGYCLEFP.GL.DDGESPEAAALRELEEE.GYKGDIAECSPAVCMDPGLSNCT
Retrocopy TLHYECIVLVKQFQPPMGGYCLEFPVGLMDDGESPEAAALRELEEEMGYKGDIAECSPAVCMDPGLSNCT

Parental  THIVTVTINGDDAENVRPKPKPGEGEFVEVISLPKNDLLKRLDALIAEEHLTVDARVYSYALAL
          THIVTVTINGDDAENVRPKPKPG.GEFVEVISLPKNDLLKRLDALIA.EHLTVDARVYSYALAL
Retrocopy THIVTVTINGDDAENVRPKPKPG-GEFVEVISLPKNDLLKRLDALIAKEHLTVDARVYSYALAL

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	0.22 RPM	13.19 RPM
SRP017611_kidney	0.41 RPM	16.52 RPM
SRP017611_liver	0.39 RPM	16.73 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_862 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_862 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019509	2 retrocopies	retro_btau_1326, retro_btau_1438,
Canis familiaris	ENSCAFG00000004794	2 retrocopies	retro_cfam_435, retro_cfam_612,
Equus caballus	ENSECAG00000023658	1 retrocopy	retro_ecab_647,
Echinops telfairi	ENSETEG00000006403	1 retrocopy	retro_etel_946,
Felis catus	ENSFCAG00000025093	1 retrocopy	retro_fcat_350,
Homo sapiens	ENSG00000165609	1 retrocopy	retro_hsap_3580,
Gorilla gorilla	ENSGGOG00000006325	1 retrocopy	retro_ggor_2415,
Loxodonta africana	ENSLAFG00000012052	1 retrocopy	retro_lafr_226,
Myotis lucifugus	ENSMLUG00000010453	2 retrocopies	retro_mluc_1263, retro_mluc_2073,
Macaca mulatta	ENSMMUG00000017141	1 retrocopy	retro_mmul_1828,
Nomascus leucogenys	ENSNLEG00000012298	1 retrocopy	retro_nleu_2838,
Oryctolagus cuniculus	ENSOCUG00000009308	1 retrocopy	retro_ocun_862 ,
Otolemur garnettii	ENSOGAG00000005816	2 retrocopies	retro_ogar_2071, retro_ogar_2988,
Pongo abelii	ENSPPYG00000002091	2 retrocopies	retro_pabe_2949, retro_pabe_3040,
Pan troglodytes	ENSPTRG00000002294	1 retrocopy	retro_ptro_2427,
Rattus norvegicus	ENSRNOG00000017741	1 retrocopy	retro_rnor_1672,
Sus scrofa	ENSSSCG00000011113	1 retrocopy	retro_sscr_143,
Tursiops truncatus	ENSTTRG00000007394	2 retrocopies	retro_ttru_209, retro_ttru_495,