RetrogeneDB ID: retro_ocun_912

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:44392764..44393243(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021780
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000012391
• Aliases: None
• Description: Ribose-phosphate pyrophosphokinase [Source:UniProtKB/TrEMBL;Acc:G1T373]

Sequence

>retro_ocun_912
ATGTCGAATGTTAAGATCTTCAGCGGCAGCTCCCACCAGGACTTATCCCAGAAAACTGCTGACCGCCTGGGCCTGGAACT
GGGCAAGGTGGTTACAAATAAATTCAGCAACCACAAGACCTGTGTGGAAACTGGCGGAAGTGTACATGGAGAGGATGTCT
ACGTTGTTCAGAGTGGTTGTGCTGAAATCAAAGACAATCTAATGGAGCTTCCAGTCATGATTAATGCCTGCAAGATTGCT
TCAGCCAGCCAGTGACGGCAGTCATCCTATGCTTCCCTTATGCTTTGCAGGATAAGGATGAGAGCTGGGCTCCAATCTCA
GCCAAGCTGTTGCAAACATGCTATCAGTGACAAGCGTCAATCCCATCATCACCATGGACCTACATGCATCTCAGATTGAG
GGCTTTTTTTGATATCCCAGTGGACAATTTGTATTTCGAGCCAGCTGTCCTGAAGTGGATCAAGGAGAACATCACAGAA

Alignment

ORF - retro_ocun_912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.04 %
• Parental protein coverage: 51.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMEL
          M.N.KIFSGSSHQDLSQK.ADRLGLELGKVVT.KFSN..TCVE.G.SV.GEDVY.VQSGC.EI.DNLMEL
Retrocopy MSNVKIFSGSSHQDLSQKTADRLGLELGKVVTNKFSNHKTCVETGGSVHGEDVYVVQSGCAEIKDNLMEL

Parental  LIMINACKIASASR-VTAVIPCFPYARQDKKDKVGESRAPISAKL-VANMLSVAGADHIITMDLHASQIQ
          ..MINACKIASAS..VTAVI.CFPYA.QDK......S.APISAKL.VANMLSV.....IITMDLHASQI.
Retrocopy PVMINACKIASASQ<VTAVILCFPYALQDKDE----SWAPISAKL<VANMLSVTSVNPIITMDLHASQIE

Parental  G-FFDIPVDNLYAEPAVLKWIKENISE
          G.FFDIPVDNLY.EPAVLKWIKENI.E
Retrocopy G>FFDIPVDNLYFEPAVLKWIKENITE

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	30.57 RPM
SRP017611_kidney	0.00 RPM	16.12 RPM
SRP017611_liver	0.00 RPM	9.79 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_912 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_912 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_912 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 27 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002784	1 retrocopy	retro_amel_22,
Bos taurus	ENSBTAG00000019703	3 retrocopies	retro_btau_157, retro_btau_1686, retro_btau_914,
Canis familiaris	ENSCAFG00000017976	1 retrocopy	retro_cfam_1443,
Dasypus novemcinctus	ENSDNOG00000002028	2 retrocopies	retro_dnov_2677, retro_dnov_947,
Dipodomys ordii	ENSDORG00000014534	2 retrocopies	retro_dord_356, retro_dord_632,
Equus caballus	ENSECAG00000024711	2 retrocopies	retro_ecab_433, retro_ecab_73,
Echinops telfairi	ENSETEG00000014736	1 retrocopy	retro_etel_267,
Felis catus	ENSFCAG00000012286	1 retrocopy	retro_fcat_394,
Homo sapiens	ENSG00000147224	1 retrocopy	retro_hsap_10,
Gorilla gorilla	ENSGGOG00000012418	1 retrocopy	retro_ggor_2583,
Macropus eugenii	ENSMEUG00000010071	2 retrocopies	retro_meug_1612, retro_meug_443,
Microcebus murinus	ENSMICG00000001929	5 retrocopies	retro_mmur_1223, retro_mmur_1422, retro_mmur_514, retro_mmur_810, retro_mmur_90,
Myotis lucifugus	ENSMLUG00000015498	2 retrocopies	retro_mluc_107, retro_mluc_356,
Macaca mulatta	ENSMMUG00000004674	3 retrocopies	retro_mmul_1204, retro_mmul_1619, retro_mmul_305,
Mustela putorius furo	ENSMPUG00000003793	2 retrocopies	retro_mputfur_183, retro_mputfur_430,
Mus musculus	ENSMUSG00000031432	2 retrocopies	retro_mmus_19, retro_mmus_33,
Nomascus leucogenys	ENSNLEG00000013911	2 retrocopies	retro_nleu_1456, retro_nleu_217,
Oryctolagus cuniculus	ENSOCUG00000012391	3 retrocopies	retro_ocun_430, retro_ocun_867, retro_ocun_912 ,
Ochotona princeps	ENSOPRG00000013140	1 retrocopy	retro_opri_704,
Pongo abelii	ENSPPYG00000020612	2 retrocopies	retro_pabe_3061, retro_pabe_46,
Pan troglodytes	ENSPTRG00000022163	2 retrocopies	retro_ptro_2600, retro_ptro_2612,
Rattus norvegicus	ENSRNOG00000025166	2 retrocopies	retro_rnor_249, retro_rnor_341,
Sus scrofa	ENSSSCG00000012560	1 retrocopy	retro_sscr_1068,
Ictidomys tridecemlineatus	ENSSTOG00000007638	2 retrocopies	retro_itri_11, retro_itri_173,
Tarsius syrichta	ENSTSYG00000013556	2 retrocopies	retro_tsyr_1063, retro_tsyr_1567,
Tursiops truncatus	ENSTTRG00000003835	2 retrocopies	retro_ttru_307, retro_ttru_485,
Vicugna pacos	ENSVPAG00000000255	1 retrocopy	retro_vpac_274,