RetrogeneDB ID: retro_ocun_1675

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018757:1476296..1476936(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000013350
• Aliases: None
• Description: None

Sequence

>retro_ocun_1675
GATCCAAACACCAAGCACTCCAGCGGCTTTGGGTTTGTCTTGTTTACCACTGTGGAGTAGGTAGATGCAGCTTATGAACA
CGAGGCCACACAAAGTGAATGGAAGCGTTGTGGGACCAAAGAGTGCCATCTCAAGAGAAGATTCTAACAGATCAGGTGCC
CACTTAACTGCGATATGAATTTTGTTGGTGGCATTAAGGAAGACACTGAAGAACATCACCTTAGAGATTATCCTAAACTA
TATGGGAAAACTGAAGTGATTAAAATCACAAATGACTGCATCAGTGGCAAGAAGAAAGGCCTTGTTTTTGTGACCTTTGA
TGACCATGACTCTATGGCTAAAGCTGTCATTTAGAAATACCGTACTGTGAACAGTCACAACTGTGAAGTAAGGAAAATCC
TGTTGAAGCAAGAGATGGCCAGTGCTTCAACCACCAGAAGAGGTATAAGTGATTCTGAGAACTTTGGTAGTGCCCGCACG
AGTGTTTTGGTGGCAATGACAACTTGAATTGTGGAAGAATTTTCAGTGATCATGGTAGCTTTGGTGGTAGCAAGGTGTTG
GTGGATATGGAGGCAGTGGAGATGTCTACGATGGGCTTGGCAGTGATGGAAGCAATTTTGGAGGTTGTAAAAGCTACAAT

Alignment

ORF - retro_ocun_1675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.58 %
• Parental protein coverage: 69.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DPNTKRSRGFGFVTYATVEEVDAA-MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKI-FVGGIKED
          DPNTK.S.GFGFV...TVE.VDAA.MN.RPHKV.G.VV.PK.A.SREDS.R.GAHLT...I.FVGGIKED
Retrocopy DPNTKHSSGFGFVLFTTVE*VDAA>MNTRPHKVNGSVVGPKSAISREDSNRSGAHLTAI*I<FVGGIKED

Parental  TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE
          TEEHHLRDY...YGK.EVI.I..D..SGKK.G..FVTFDDHDS..K.VI.KY.TVN.HNCEVRK.L.KQE
Retrocopy TEEHHLRDYPKLYGKTEVIKITNDCISGKKKGLVFVTFDDHDSMAKAVI*KYRTVNSHNCEVRKILLKQE

Parental  MASASSTPRGRSGSGNFGGGRGG-GFGGNDNFGRGGNFSGRGGFGGSR-GGGGYGGSGDGYNGFGNDEGS
          MASAS.T.RG.S.S.NFG..R....FGGNDN...G..FS..G.FGGS..G.GGYGGSGD.Y.G.G.D.GS
Retrocopy MASASTTRRGISDSENFGSARTS<CFGGNDNLNCGRIFSDHGSFGGSK<GVGGYGGSGDVYDGLGSD-GS

Parental  GYGGSGSYD
          ..GG..SY.
Retrocopy NFGGCKSYN

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	163.30 RPM
SRP017611_kidney	0.00 RPM	196.12 RPM
SRP017611_liver	0.00 RPM	105.90 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1675 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1675 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 32 parental genes, and 299 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000717	3 retrocopies	retro_amel_1726, retro_amel_547, retro_amel_925,
Bos taurus	ENSBTAG00000001553	20 retrocopies	retro_btau_1019, retro_btau_1065, retro_btau_1268, retro_btau_1378, retro_btau_1379, retro_btau_1437, retro_btau_1455, retro_btau_1657, retro_btau_1673, retro_btau_283, retro_btau_337, retro_btau_403, retro_btau_462, retro_btau_516, retro_btau_519, retro_btau_589, retro_btau_602, retro_btau_677, retro_btau_715, retro_btau_822,
Canis familiaris	ENSCAFG00000006580	16 retrocopies	retro_cfam_1080, retro_cfam_1081, retro_cfam_1170, retro_cfam_1323, retro_cfam_1616, retro_cfam_1844, retro_cfam_2017, retro_cfam_2128, retro_cfam_360, retro_cfam_564, retro_cfam_702, retro_cfam_803, retro_cfam_839, retro_cfam_855, retro_cfam_892, retro_cfam_937,
Cavia porcellus	ENSCPOG00000020972	1 retrocopy	retro_cpor_1078,
Dasypus novemcinctus	ENSDNOG00000009228	7 retrocopies	retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Equus caballus	ENSECAG00000008676	1 retrocopy	retro_ecab_74,
Felis catus	ENSFCAG00000010150	9 retrocopies	retro_fcat_1574, retro_fcat_1742, retro_fcat_1867, retro_fcat_382, retro_fcat_474, retro_fcat_712, retro_fcat_781, retro_fcat_844, retro_fcat_888,
Homo sapiens	ENSG00000135486	57 retrocopies	retro_hsap_1021, retro_hsap_1042, retro_hsap_1082, retro_hsap_1240, retro_hsap_1276, retro_hsap_1282, retro_hsap_1287, retro_hsap_1481, retro_hsap_158, retro_hsap_1584, retro_hsap_1613, retro_hsap_1638, retro_hsap_1711, retro_hsap_1899, retro_hsap_1933, retro_hsap_2002, retro_hsap_2029, retro_hsap_2091, retro_hsap_2096, retro_hsap_2197, retro_hsap_2347, retro_hsap_2379, retro_hsap_2636, retro_hsap_2640, retro_hsap_2668, retro_hsap_2718, retro_hsap_2857, retro_hsap_291, retro_hsap_2917, retro_hsap_2944, retro_hsap_3049, retro_hsap_3055, retro_hsap_332, retro_hsap_3343, retro_hsap_3393, retro_hsap_3432, retro_hsap_3439, retro_hsap_3449, retro_hsap_3549, retro_hsap_3745, retro_hsap_3756, retro_hsap_3757, retro_hsap_394, retro_hsap_3979, retro_hsap_4011, retro_hsap_4084, retro_hsap_414, retro_hsap_4218, retro_hsap_4282, retro_hsap_437, retro_hsap_4747, retro_hsap_482, retro_hsap_4883, retro_hsap_668, retro_hsap_84, retro_hsap_845, retro_hsap_924,
Gorilla gorilla	ENSGGOG00000003040	6 retrocopies	retro_ggor_1006, retro_ggor_1010, retro_ggor_1221, retro_ggor_1738, retro_ggor_2041, retro_ggor_950,
Loxodonta africana	ENSLAFG00000029587	5 retrocopies	retro_lafr_1202, retro_lafr_1208, retro_lafr_192, retro_lafr_747, retro_lafr_961,
Myotis lucifugus	ENSMLUG00000000648	3 retrocopies	retro_mluc_2503, retro_mluc_342, retro_mluc_82,
Macaca mulatta	ENSMMUG00000012989	5 retrocopies	retro_mmul_1031, retro_mmul_1427, retro_mmul_1726, retro_mmul_187, retro_mmul_1871,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Mus musculus	ENSMUSG00000046434	3 retrocopies	retro_mmus_1861, retro_mmus_410, retro_mmus_543,
Nomascus leucogenys	ENSNLEG00000017659	34 retrocopies	retro_nleu_1011, retro_nleu_1090, retro_nleu_1257, retro_nleu_130, retro_nleu_132, retro_nleu_1497, retro_nleu_1630, retro_nleu_1648, retro_nleu_166, retro_nleu_167, retro_nleu_1695, retro_nleu_1739, retro_nleu_1774, retro_nleu_1802, retro_nleu_1875, retro_nleu_190, retro_nleu_2040, retro_nleu_2222, retro_nleu_2304, retro_nleu_2324, retro_nleu_2378, retro_nleu_2690, retro_nleu_2742, retro_nleu_2852, retro_nleu_32, retro_nleu_366, retro_nleu_458, retro_nleu_587, retro_nleu_601, retro_nleu_645, retro_nleu_648, retro_nleu_708, retro_nleu_825, retro_nleu_987,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675 ,
Oryctolagus cuniculus	ENSOCUG00000013805	1 retrocopy	retro_ocun_505,
Oryctolagus cuniculus	ENSOCUG00000026424	3 retrocopies	retro_ocun_1800, retro_ocun_1811, retro_ocun_950,
Oryctolagus cuniculus	ENSOCUG00000026859	2 retrocopies	retro_ocun_1205, retro_ocun_642,
Otolemur garnettii	ENSOGAG00000029707	3 retrocopies	retro_ogar_1721, retro_ogar_205, retro_ogar_2321,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,
Ochotona princeps	ENSOPRG00000006107	10 retrocopies	retro_opri_1183, retro_opri_338, retro_opri_349, retro_opri_424, retro_opri_456, retro_opri_597, retro_opri_753, retro_opri_782, retro_opri_79, retro_opri_843,
Procavia capensis	ENSPCAG00000001867	5 retrocopies	retro_pcap_111, retro_pcap_162, retro_pcap_377, retro_pcap_424, retro_pcap_435,
Pongo abelii	ENSPPYG00000025850	4 retrocopies	retro_pabe_1765, retro_pabe_2285, retro_pabe_3492, retro_pabe_3835,
Pteropus vampyrus	ENSPVAG00000000322	9 retrocopies	retro_pvam_1133, retro_pvam_1230, retro_pvam_1313, retro_pvam_1370, retro_pvam_196, retro_pvam_300, retro_pvam_453, retro_pvam_643, retro_pvam_859,
Rattus norvegicus	ENSRNOG00000036839	17 retrocopies	retro_rnor_1001, retro_rnor_1322, retro_rnor_1658, retro_rnor_1770, retro_rnor_1786, retro_rnor_1846, retro_rnor_1987, retro_rnor_2194, retro_rnor_2482, retro_rnor_2551, retro_rnor_2619, retro_rnor_2657, retro_rnor_2881, retro_rnor_2944, retro_rnor_2945, retro_rnor_2965, retro_rnor_2969,
Sus scrofa	ENSSSCG00000000288	3 retrocopies	retro_sscr_354, retro_sscr_355, retro_sscr_861,
Ictidomys tridecemlineatus	ENSSTOG00000006551	8 retrocopies	retro_itri_1291, retro_itri_1567, retro_itri_190, retro_itri_354, retro_itri_439, retro_itri_446, retro_itri_456, retro_itri_515,
Tupaia belangeri	ENSTBEG00000008238	30 retrocopies	retro_tbel_1219, retro_tbel_156, retro_tbel_162, retro_tbel_1643, retro_tbel_1830, retro_tbel_1967, retro_tbel_2192, retro_tbel_2195, retro_tbel_2211, retro_tbel_2330, retro_tbel_261, retro_tbel_2666, retro_tbel_2673, retro_tbel_2703, retro_tbel_276, retro_tbel_2774, retro_tbel_2787, retro_tbel_2970, retro_tbel_3473, retro_tbel_3976, retro_tbel_3995, retro_tbel_4266, retro_tbel_4271, retro_tbel_453, retro_tbel_4653, retro_tbel_4729, retro_tbel_692, retro_tbel_70, retro_tbel_79, retro_tbel_839,
Tursiops truncatus	ENSTTRG00000004505	27 retrocopies	retro_ttru_1202, retro_ttru_1223, retro_ttru_1251, retro_ttru_1331, retro_ttru_1362, retro_ttru_156, retro_ttru_157, retro_ttru_1678, retro_ttru_1732, retro_ttru_1806, retro_ttru_1813, retro_ttru_1874, retro_ttru_221, retro_ttru_311, retro_ttru_479, retro_ttru_599, retro_ttru_605, retro_ttru_607, retro_ttru_620, retro_ttru_63, retro_ttru_678, retro_ttru_708, retro_ttru_812, retro_ttru_882, retro_ttru_902, retro_ttru_926, retro_ttru_981,