RetrogeneDB ID: retro_ocun_990

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:39146916..39147465(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000028017
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUDT9
• Ensembl ID: ENSOCUG00000002670
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 9 [Source:HGNC Symbol;Acc:8056]

Sequence

>retro_ocun_990
GCAGGTTGGTCAGGCCCAGTTGGCCCTGGGCTCTAGGAGCACTGGGGCCCCAATCATGTTGCTGATCCTATCCTAACCAG
CTGGAGAAAGGATAGCAAGGGAAATCACATTACTCATCCTATTTCTGGGAAAAAAAAAAACACCCTGCAAGTTGTAGACA
TCAAAAGGAAGAATTGTGGAGAATGGGCCATCCCAGGTAGGGTGAGGGATCCAGCAGAGAAGATGACTGCTGCTCTGAAG
AGAGAGTTTGGCGGGGAAGCCAGGAACTCCTTACAGAAATCCGGGGCAGAAAGGCAGGAGTTGGAGGAACAATTGCACCT
GCTCTTCAGCCAGAAACAGTTTGAGGTCTGTAAGGACTATGTGGATGGTCCTCGCAACACAGACAATGCATGGAGGGAGA
CGCAGGCTGTGAGCTACCACGATGACACAGGGGAAATAACGGAGCATCTTCCTGTGGAAGCTGGCGATGACGCTGCGGGA
GTGAACTGGGTGGACATAAGTGATAGACCCAAGTTGCATGCCAGCCACTCCCAGTGTATTCATGTTTTG

Alignment

ORF - retro_ocun_990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.48 %
• Parental protein coverage: 51.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGRTGLVGRGLLGRWGPNHAADPIITRWKKNNSGNKITHPVSGK--HILQFVAIKRKDCGEWAIPGGMVD
          AG..G.VG.GL...WGPNH.ADPI.T.W.K...GN.ITHP.SGK....LQ.V.IKRK.CGEWAIPG...D
Retrocopy AGWSGPVGPGL*EHWGPNHVADPILTSWRKDSKGNHITHPISGKKKNTLQVVDIKRKNCGEWAIPGRVRD

Parental  PGEKISAALKREFGEEALNSLQKSSAEKIEIEKQLHRLFSQDHLVIYKGYVDDPRNTDNAWVETEAVNYH
          P.EK..AALKREFG.EA.NSLQKS.AE..E.E.QLH.LFSQ......K.YVD.PRNTDNAW.ET.AV.YH
Retrocopy PAEKMTAALKREFGGEARNSLQKSGAERQELEEQLHLLFSQKQFEVCKDYVDGPRNTDNAWRETQAVSYH

Parental  DETGEIMDSITLEAGDDAGKVKWVDISDKLKLYASHSQFIKLV
          D.TGEI......EAGDDA..V.WVDISD..KL.ASHSQ.I...
Retrocopy DDTGEITEHLPVEAGDDAAGVNWVDISDRPKLHASHSQCIHVL

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	51.88 RPM
SRP017611_kidney	0.00 RPM	8.72 RPM
SRP017611_liver	0.00 RPM	5.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_990 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_990 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_990 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_709
Pan troglodytes	retro_ptro_506
Gorilla gorilla	retro_ggor_602
Pongo abelii	retro_pabe_613
Callithrix jacchus	retro_cjac_1047
Bos taurus	retro_btau_1112
Sus scrofa	retro_sscr_447
Canis familiaris	retro_cfam_1271
Equus caballus	retro_ecab_123

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003244	1 retrocopy	retro_amel_612,
Bos taurus	ENSBTAG00000011354	1 retrocopy	retro_btau_1112,
Canis familiaris	ENSCAFG00000009529	1 retrocopy	retro_cfam_1271,
Callithrix jacchus	ENSCJAG00000006159	1 retrocopy	retro_cjac_1047,
Ciona savignyi	ENSCSAVG00000008837	1 retrocopy	retro_csav_15,
Equus caballus	ENSECAG00000019556	1 retrocopy	retro_ecab_123,
Echinops telfairi	ENSETEG00000019164	1 retrocopy	retro_etel_348,
Felis catus	ENSFCAG00000003315	1 retrocopy	retro_fcat_1509,
Homo sapiens	ENSG00000170502	1 retrocopy	retro_hsap_709,
Gorilla gorilla	ENSGGOG00000014777	1 retrocopy	retro_ggor_602,
Loxodonta africana	ENSLAFG00000011391	1 retrocopy	retro_lafr_224,
Macropus eugenii	ENSMEUG00000012123	4 retrocopies	retro_meug_1072, retro_meug_1345, retro_meug_1758, retro_meug_2162,
Monodelphis domestica	ENSMODG00000020738	2 retrocopies	retro_mdom_157, retro_mdom_706,
Mustela putorius furo	ENSMPUG00000002258	1 retrocopy	retro_mputfur_585,
Nomascus leucogenys	ENSNLEG00000009520	1 retrocopy	retro_nleu_464,
Oryctolagus cuniculus	ENSOCUG00000002670	2 retrocopies	retro_ocun_1045, retro_ocun_990 ,
Ochotona princeps	ENSOPRG00000004055	1 retrocopy	retro_opri_1152,
Pongo abelii	ENSPPYG00000014914	1 retrocopy	retro_pabe_613,
Pan troglodytes	ENSPTRG00000016259	1 retrocopy	retro_ptro_506,
Pteropus vampyrus	ENSPVAG00000004829	1 retrocopy	retro_pvam_475,
Sus scrofa	ENSSSCG00000009223	1 retrocopy	retro_sscr_447,
Tursiops truncatus	ENSTTRG00000004207	1 retrocopy	retro_ttru_1549,
Vicugna pacos	ENSVPAG00000004012	1 retrocopy	retro_vpac_125,