RetrogeneDB ID: retro_ocun_1580

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018702:6796313..6796654(+)
• Located in intron of: ENSOCUG00000017848

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000017386
• Aliases: None
• Description: None

Sequence

>retro_ocun_1580
GTGGCAGCGAAGAGGATGAAAAAGCCATTGGAGTCGATCAACTCTAGACTCCAGCTTGTGACACAGAGTGGGAGATACTT
GCCAGCTACACATAGACTCTGAAGATGGTAAGACAAGGCAAAGTGAAACTGGCCATCCTCACCAGTAACACCCTGGCTTT
GAGGAAATCTGAAATAGAGTATTCTGTCAGGTTCACCAAAACAGGTGTCCATTGCTATAGTGGCAATAATCCTGAACTGG
GCACAATGTGTGGAAAATACTACAGCTTATGCACCCTTTCTCTCCTGGATCCAGATGATTCTGATGTTATTAGAAGCTTG
CCAGAACAGACTGATGAAAAG

Alignment

ORF - retro_ocun_1580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.7 %
• Parental protein coverage: 99.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAAKKTKKSLESINSRLQLVMKSGKYV-LGYKQSLKMIRQGKAKLVILANNCPALRKSEIEYYAMLAKTG
          VAAK..KK.LESINSRLQLV..SG.Y....Y...LKM.RQGK.KL.IL..N..ALRKSEIEY.....KTG
Retrocopy VAAKRMKKPLESINSRLQLVTQSGRYL<ASYT*TLKMVRQGKVKLAILTSNTLALRKSEIEYSVRFTKTG

Parental  VHHYSGNNIELGTACGKYYRVCTLSIIDPGDSDIIRSMPEQTGEK
          VH.YSGNN.ELGT.CGKYY..CTLS..DP.DSD.IRS.PEQT.EK
Retrocopy VHCYSGNNPELGTMCGKYYSLCTLSLLDPDDSDVIRSLPEQTDEK

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	55.30 RPM
SRP017611_kidney	0.00 RPM	100.75 RPM
SRP017611_liver	0.00 RPM	52.64 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1580 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1580 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1580 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 205 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016047	2 retrocopies	retro_acar_170, retro_acar_47,
Ailuropoda melanoleuca	ENSAMEG00000000605	18 retrocopies	retro_amel_1007, retro_amel_1148, retro_amel_1205, retro_amel_1456, retro_amel_1490, retro_amel_1596, retro_amel_1709, retro_amel_1738, retro_amel_26, retro_amel_384, retro_amel_40, retro_amel_456, retro_amel_50, retro_amel_534, retro_amel_551, retro_amel_642, retro_amel_745, retro_amel_806,
Bos taurus	ENSBTAG00000016278	2 retrocopies	retro_btau_34, retro_btau_992,
Callithrix jacchus	ENSCJAG00000015549	4 retrocopies	retro_cjac_14, retro_cjac_253, retro_cjac_320, retro_cjac_351,
Cavia porcellus	ENSCPOG00000026030	4 retrocopies	retro_cpor_1287, retro_cpor_1325, retro_cpor_505, retro_cpor_764,
Dasypus novemcinctus	ENSDNOG00000013828	12 retrocopies	retro_dnov_1331, retro_dnov_1754, retro_dnov_1883, retro_dnov_2094, retro_dnov_2208, retro_dnov_2455, retro_dnov_2484, retro_dnov_2513, retro_dnov_2670, retro_dnov_293, retro_dnov_334, retro_dnov_415,
Dipodomys ordii	ENSDORG00000012383	10 retrocopies	retro_dord_111, retro_dord_204, retro_dord_361, retro_dord_407, retro_dord_49, retro_dord_69, retro_dord_710, retro_dord_736, retro_dord_83, retro_dord_97,
Equus caballus	ENSECAG00000021705	7 retrocopies	retro_ecab_1094, retro_ecab_227, retro_ecab_406, retro_ecab_508, retro_ecab_599, retro_ecab_63, retro_ecab_945,
Erinaceus europaeus	ENSEEUG00000000964	9 retrocopies	retro_eeur_137, retro_eeur_214, retro_eeur_237, retro_eeur_355, retro_eeur_432, retro_eeur_59, retro_eeur_614, retro_eeur_69, retro_eeur_83,
Felis catus	ENSFCAG00000002165	9 retrocopies	retro_fcat_1261, retro_fcat_1391, retro_fcat_1473, retro_fcat_1689, retro_fcat_1872, retro_fcat_323, retro_fcat_45, retro_fcat_49, retro_fcat_754,
Homo sapiens	ENSG00000156482	9 retrocopies	retro_hsap_1104, retro_hsap_1947, retro_hsap_2229, retro_hsap_2767, retro_hsap_3509, retro_hsap_3959, retro_hsap_4000, retro_hsap_4652, retro_hsap_475,
Gorilla gorilla	ENSGGOG00000005502	9 retrocopies	retro_ggor_1416, retro_ggor_1663, retro_ggor_178, retro_ggor_1925, retro_ggor_2661, retro_ggor_2886, retro_ggor_3073, retro_ggor_46, retro_ggor_866,
Loxodonta africana	ENSLAFG00000002077	2 retrocopies	retro_lafr_122, retro_lafr_882,
Microcebus murinus	ENSMICG00000004620	3 retrocopies	retro_mmur_258, retro_mmur_644, retro_mmur_693,
Myotis lucifugus	ENSMLUG00000003637	11 retrocopies	retro_mluc_1425, retro_mluc_2001, retro_mluc_2274, retro_mluc_2295, retro_mluc_2409, retro_mluc_409, retro_mluc_583, retro_mluc_639, retro_mluc_827, retro_mluc_838, retro_mluc_894,
Macaca mulatta	ENSMMUG00000020073	12 retrocopies	retro_mmul_1353, retro_mmul_2275, retro_mmul_2291, retro_mmul_2309, retro_mmul_2322, retro_mmul_2473, retro_mmul_29, retro_mmul_319, retro_mmul_416, retro_mmul_576, retro_mmul_663, retro_mmul_857,
Monodelphis domestica	ENSMODG00000006804	1 retrocopy	retro_mdom_664,
Mus musculus	ENSMUSG00000058600	21 retrocopies	retro_mmus_1048, retro_mmus_1102, retro_mmus_1276, retro_mmus_1434, retro_mmus_1439, retro_mmus_1586, retro_mmus_2059, retro_mmus_2273, retro_mmus_2728, retro_mmus_2828, retro_mmus_3179, retro_mmus_3286, retro_mmus_342, retro_mmus_3465, retro_mmus_3573, retro_mmus_3583, retro_mmus_3681, retro_mmus_3691, retro_mmus_569, retro_mmus_789, retro_mmus_892,
Oryctolagus cuniculus	ENSOCUG00000017386	4 retrocopies	retro_ocun_1447, retro_ocun_1580 , retro_ocun_178, retro_ocun_279,
Ochotona princeps	ENSOPRG00000007644	3 retrocopies	retro_opri_1087, retro_opri_662, retro_opri_954,
Pongo abelii	ENSPPYG00000018774	4 retrocopies	retro_pabe_1605, retro_pabe_178, retro_pabe_2846, retro_pabe_8,
Pan troglodytes	ENSPTRG00000020454	10 retrocopies	retro_ptro_1146, retro_ptro_1302, retro_ptro_1575, retro_ptro_1874, retro_ptro_2334, retro_ptro_2380, retro_ptro_2688, retro_ptro_3091, retro_ptro_356, retro_ptro_693,
Pteropus vampyrus	ENSPVAG00000014461	9 retrocopies	retro_pvam_1079, retro_pvam_1090, retro_pvam_1099, retro_pvam_161, retro_pvam_276, retro_pvam_279, retro_pvam_407, retro_pvam_506, retro_pvam_561,
Rattus norvegicus	ENSRNOG00000005975	19 retrocopies	retro_rnor_1, retro_rnor_1038, retro_rnor_1631, retro_rnor_1812, retro_rnor_1830, retro_rnor_1876, retro_rnor_1893, retro_rnor_1946, retro_rnor_1975, retro_rnor_2211, retro_rnor_2598, retro_rnor_2636, retro_rnor_2666, retro_rnor_2736, retro_rnor_739, retro_rnor_745, retro_rnor_753, retro_rnor_761, retro_rnor_940,
Sus scrofa	ENSSSCG00000006081	6 retrocopies	retro_sscr_100, retro_sscr_1211, retro_sscr_778, retro_sscr_782, retro_sscr_876, retro_sscr_963,
Tursiops truncatus	ENSTTRG00000016058	5 retrocopies	retro_ttru_167, retro_ttru_1871, retro_ttru_1908, retro_ttru_1941, retro_ttru_509,