RetrogeneDB ID: retro_ocun_1137

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 20:30903899..30904191(+)
• Located in intron of: ENSOCUG00000017491

Retrocopy information

• Ensembl ID: ENSOCUG00000007176
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSOCUG00000023645
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_ocun_1137
AAGGGCCTTTTCGGCGGAAAGGAAATGTGTCCCCTCGTGGCGGGCCTGGATGCTGCGGGGAAGACGACGATGCCGGACAA
GCAGAAGCTCGGGGAAACTGTGACCACCTCCCCACCGTGGGCTTCAACGTGGGGACTGTGGAGCACACGAGCGTCAGCCC
CACGTGTGGGGCGTGGGCGGCCAGGCCCAGATTCGGCCGCTGCGGCACCACTACTTCCGGAACACCCAAGCCTTACTCTT
TGCGGTGGCCAGCAATGACCGAGAGCGTGTGCATGAGGTGCGGGAGGAGCTC

Alignment

ORF - retro_ocun_1137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.0 %
• Parental protein coverage: 54.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTT-IPTIGFNVETVEYKNISFT-VWDVGGQDKIRPL
          KGLFG.KEM..L..GLDAAGKTT...K.KLGE.VTT..PT.GFNV.TVE....S.T.VW.VGGQ..IRPL
Retrocopy KGLFGGKEMCPLVAGLDAAGKTTMPDKQKLGETVTT<LPTVGFNVGTVEHTSVSPT<VWGVGGQAQIRPL

Parental  WRHYFQNTQGLIFVVDSNDRERVNEAREEL
          ..HYF.NTQ.L.F.V.SNDRERV.E.REEL
Retrocopy RHHYFRNTQALLFAVASNDRERVHEVREEL

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	79.36 RPM
SRP017611_kidney	0.00 RPM	83.42 RPM
SRP017611_liver	0.00 RPM	29.21 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1137 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1137 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1137 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 36 parental genes, and 95 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000004509	1 retrocopy	retro_apla_4,
Bos taurus	ENSBTAG00000007725	2 retrocopies	retro_btau_1257, retro_btau_1390,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Cavia porcellus	ENSCPOG00000021174	1 retrocopy	retro_cpor_1310,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Dasypus novemcinctus	ENSDNOG00000010454	3 retrocopies	retro_dnov_2375, retro_dnov_2459, retro_dnov_26,
Erinaceus europaeus	ENSEEUG00000004638	4 retrocopies	retro_eeur_328, retro_eeur_660, retro_eeur_684, retro_eeur_76,
Ficedula albicollis	ENSFALG00000001088	1 retrocopy	retro_falb_2,
Felis catus	ENSFCAG00000029374	1 retrocopy	retro_fcat_1829,
Homo sapiens	ENSG00000143761	3 retrocopies	retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Gorilla gorilla	ENSGGOG00000011263	5 retrocopies	retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Mus musculus	ENSMUSG00000048076	1 retrocopy	retro_mmus_1718,
Nomascus leucogenys	ENSNLEG00000014137	3 retrocopies	retro_nleu_210, retro_nleu_227, retro_nleu_2929,
Oryctolagus cuniculus	ENSOCUG00000000824	4 retrocopies	retro_ocun_1007, retro_ocun_1502, retro_ocun_1868, retro_ocun_987,
Oryctolagus cuniculus	ENSOCUG00000014090	2 retrocopies	retro_ocun_1942, retro_ocun_751,
Oryctolagus cuniculus	ENSOCUG00000023009	1 retrocopy	retro_ocun_1404,
Oryctolagus cuniculus	ENSOCUG00000023198	1 retrocopy	retro_ocun_132,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137 , retro_ocun_247,
Otolemur garnettii	ENSOGAG00000010974	4 retrocopies	retro_ogar_2431, retro_ogar_295, retro_ogar_3353, retro_ogar_974,
Ochotona princeps	ENSOPRG00000015063	2 retrocopies	retro_opri_317, retro_opri_759,
Pongo abelii	ENSPPYG00000000148	3 retrocopies	retro_pabe_3159, retro_pabe_849, retro_pabe_965,
Pelodiscus sinensis	ENSPSIG00000009767	1 retrocopy	retro_psin_12,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Pteropus vampyrus	ENSPVAG00000007383	1 retrocopy	retro_pvam_1324,
Rattus norvegicus	ENSRNOG00000030591	3 retrocopies	retro_rnor_1268, retro_rnor_1348, retro_rnor_1950,
Sarcophilus harrisii	ENSSHAG00000014599	3 retrocopies	retro_shar_106, retro_shar_462, retro_shar_725,
Sus scrofa	ENSSSCG00000013992	2 retrocopies	retro_sscr_429, retro_sscr_82,
Ictidomys tridecemlineatus	ENSSTOG00000009288	3 retrocopies	retro_itri_1754, retro_itri_273, retro_itri_363,
Tupaia belangeri	ENSTBEG00000009218	9 retrocopies	retro_tbel_1943, retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Taeniopygia guttata	ENSTGUG00000000233	1 retrocopy	retro_tgut_2,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000014186	2 retrocopies	retro_ttru_1679, retro_ttru_347,
Vicugna pacos	ENSVPAG00000003224	4 retrocopies	retro_vpac_281, retro_vpac_328, retro_vpac_6, retro_vpac_78,