RetrogeneDB ID: retro_sscr_263

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 11:34342962..34343257(+)
• Located in intron of: ENSSSCG00000021189

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL31
• Ensembl ID: ENSSSCG00000008170
• Aliases: None
• Description: 60S ribosomal protein L31 [Source:UniProtKB/Swiss-Prot;Acc:P62901]

Sequence

>retro_sscr_263
GTGGTGACCAGAAGATACACCAGCAGCATTCAAAGCACATCCATGGAGTGGGCTTAAAGACATCTGCCCTTCAGACACTC
AAGGAAACTGGAAGTCCTCGGTGAAGGAGATGGGAACTCCAGATGTGTACACTGACACCAGGCTCAACAAACCTGTTTAG
GCCAAAGGAATAGGAATGCCCCACACTATCCATGTGTGGTTGTTCAGAACATGTAACAAGGATGAAGACTCACCAAGAAG
ACTCTATTTGCTGGTTATGGATGTTCCTGTCACCACTTTCCAAAATCTACATTCA

Alignment

ORF - retro_sscr_263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.8 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVTREYTINIH-KRIHGVGFKKRAPRALKEIR-KFAMKEMGTPDVRIDTRLNKAVWAKGIRNVPYRIRVR
          VVTR.YT..I..K.IHGVG.K..A...LKE...K...KEMGTPDV..DTRLNK.V.AKGI...P..I.V.
Retrocopy VVTRRYTSSIQ<KHIHGVGLKTSALQTLKETG<KSSVKEMGTPDVYTDTRLNKPV*AKGI-GMPHTIHVW

Parental  LSRKRNEDEDSPNKLYTLVTYVPVTTFKNLQT
          L.R..N.DEDSP..LY.LV..VPVTTF.NL..
Retrocopy LFRTCNKDEDSPRRLYLLVMDVPVTTFQNLHS

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
SRP014902_placenta	0.00 RPM	0.80 RPM
SRP014902_testis	0.00 RPM	9.34 RPM
SRP018288_heart	0.00 RPM	3.90 RPM
SRP018288_kidney	0.00 RPM	2.36 RPM
SRP018288_liver	0.00 RPM	2.88 RPM
SRP018288_lung	0.00 RPM	1.02 RPM
SRP018856_adipose	0.00 RPM	3.18 RPM
SRP035408_brain	0.00 RPM	1.68 RPM
SRP035408_liver	0.00 RPM	1.59 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_263 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_263 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 343 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000007914	1 retrocopy	retro_acar_168,
Ailuropoda melanoleuca	ENSAMEG00000015647	2 retrocopies	retro_amel_12, retro_amel_222,
Cavia porcellus	ENSCPOG00000021031	5 retrocopies	retro_cpor_1184, retro_cpor_170, retro_cpor_190, retro_cpor_341, retro_cpor_366,
Dipodomys ordii	ENSDORG00000015728	3 retrocopies	retro_dord_164, retro_dord_515, retro_dord_770,
Equus caballus	ENSECAG00000024079	13 retrocopies	retro_ecab_1034, retro_ecab_1102, retro_ecab_163, retro_ecab_206, retro_ecab_259, retro_ecab_332, retro_ecab_397, retro_ecab_414, retro_ecab_448, retro_ecab_451, retro_ecab_499, retro_ecab_812, retro_ecab_972,
Felis catus	ENSFCAG00000026430	13 retrocopies	retro_fcat_1420, retro_fcat_148, retro_fcat_17, retro_fcat_190, retro_fcat_1957, retro_fcat_2003, retro_fcat_251, retro_fcat_46, retro_fcat_466, retro_fcat_658, retro_fcat_725, retro_fcat_803, retro_fcat_881,
Latimeria chalumnae	ENSLACG00000013603	1 retrocopy	retro_lcha_94,
Loxodonta africana	ENSLAFG00000027873	12 retrocopies	retro_lafr_118, retro_lafr_187, retro_lafr_20, retro_lafr_245, retro_lafr_307, retro_lafr_56, retro_lafr_663, retro_lafr_703, retro_lafr_710, retro_lafr_778, retro_lafr_885, retro_lafr_926,
Macropus eugenii	ENSMEUG00000000963	8 retrocopies	retro_meug_1083, retro_meug_1433, retro_meug_1731, retro_meug_1741, retro_meug_198, retro_meug_418, retro_meug_588, retro_meug_649,
Myotis lucifugus	ENSMLUG00000002507	21 retrocopies	retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Monodelphis domestica	ENSMODG00000001704	5 retrocopies	retro_mdom_1052, retro_mdom_1464, retro_mdom_1674, retro_mdom_1720, retro_mdom_1818,
Mustela putorius furo	ENSMPUG00000012197	2 retrocopies	retro_mputfur_50, retro_mputfur_71,
Otolemur garnettii	ENSOGAG00000014494	10 retrocopies	retro_ogar_103, retro_ogar_143, retro_ogar_150, retro_ogar_178, retro_ogar_181, retro_ogar_186, retro_ogar_262, retro_ogar_271, retro_ogar_29, retro_ogar_3,
Ochotona princeps	ENSOPRG00000001204	34 retrocopies	retro_opri_1032, retro_opri_1059, retro_opri_1081, retro_opri_1108, retro_opri_1117, retro_opri_113, retro_opri_1176, retro_opri_1177, retro_opri_132, retro_opri_152, retro_opri_179, retro_opri_213, retro_opri_236, retro_opri_259, retro_opri_346, retro_opri_411, retro_opri_435, retro_opri_531, retro_opri_561, retro_opri_572, retro_opri_58, retro_opri_588, retro_opri_602, retro_opri_677, retro_opri_710, retro_opri_744, retro_opri_796, retro_opri_803, retro_opri_804, retro_opri_811, retro_opri_819, retro_opri_909, retro_opri_915, retro_opri_93,
Procavia capensis	ENSPCAG00000004787	10 retrocopies	retro_pcap_121, retro_pcap_125, retro_pcap_152, retro_pcap_228, retro_pcap_230, retro_pcap_266, retro_pcap_33, retro_pcap_378, retro_pcap_401, retro_pcap_413,
Pongo abelii	ENSPPYG00000025870	4 retrocopies	retro_pabe_106, retro_pabe_1635, retro_pabe_168, retro_pabe_895,
Pteropus vampyrus	ENSPVAG00000011716	17 retrocopies	retro_pvam_1131, retro_pvam_1265, retro_pvam_1359, retro_pvam_197, retro_pvam_349, retro_pvam_410, retro_pvam_441, retro_pvam_469, retro_pvam_484, retro_pvam_501, retro_pvam_565, retro_pvam_606, retro_pvam_631, retro_pvam_65, retro_pvam_815, retro_pvam_861, retro_pvam_864,
Rattus norvegicus	ENSRNOG00000013508	8 retrocopies	retro_rnor_101, retro_rnor_152, retro_rnor_1809, retro_rnor_217, retro_rnor_22, retro_rnor_267, retro_rnor_277, retro_rnor_286,
Sarcophilus harrisii	ENSSHAG00000011706	3 retrocopies	retro_shar_190, retro_shar_285, retro_shar_721,
Sus scrofa	ENSSSCG00000008170	4 retrocopies	retro_sscr_1072, retro_sscr_1073, retro_sscr_128, retro_sscr_263 ,
Sus scrofa	ENSSSCG00000025180	6 retrocopies	retro_sscr_20, retro_sscr_34, retro_sscr_469, retro_sscr_501, retro_sscr_713, retro_sscr_81,
Tupaia belangeri	ENSTBEG00000016254	137 retrocopies	retro_tbel_1092, retro_tbel_1129, retro_tbel_115, retro_tbel_1176, retro_tbel_1195, retro_tbel_1226, retro_tbel_1239, retro_tbel_1249, retro_tbel_1254, retro_tbel_1258, retro_tbel_1266, retro_tbel_131, retro_tbel_1310, retro_tbel_1334, retro_tbel_1356, retro_tbel_1368, retro_tbel_1369, retro_tbel_1381, retro_tbel_1402, retro_tbel_1414, retro_tbel_1423, retro_tbel_1437, retro_tbel_1454, retro_tbel_1574, retro_tbel_1593, retro_tbel_1597, retro_tbel_1605, retro_tbel_1611, retro_tbel_1612, retro_tbel_1632, retro_tbel_1768, retro_tbel_1797, retro_tbel_1802, retro_tbel_184, retro_tbel_189, retro_tbel_1890, retro_tbel_1897, retro_tbel_1915, retro_tbel_2024, retro_tbel_2027, retro_tbel_2050, retro_tbel_2069, retro_tbel_2093, retro_tbel_2140, retro_tbel_2159, retro_tbel_2233, retro_tbel_2341, retro_tbel_2359, retro_tbel_2382, retro_tbel_246, retro_tbel_2520, retro_tbel_2531, retro_tbel_2581, retro_tbel_2582, retro_tbel_2614, retro_tbel_2625, retro_tbel_2668, retro_tbel_2692, retro_tbel_2709, retro_tbel_2741, retro_tbel_2789, retro_tbel_2825, retro_tbel_2847, retro_tbel_2930, retro_tbel_2951, retro_tbel_3015, retro_tbel_3028, retro_tbel_3035, retro_tbel_3061, retro_tbel_3077, retro_tbel_3154, retro_tbel_3174, retro_tbel_3222, retro_tbel_3274, retro_tbel_3282, retro_tbel_3292, retro_tbel_3346, retro_tbel_3365, retro_tbel_337, retro_tbel_3378, retro_tbel_3425, retro_tbel_3442, retro_tbel_3484, retro_tbel_3500, retro_tbel_3519, retro_tbel_3578, retro_tbel_3580, retro_tbel_3618, retro_tbel_3637, retro_tbel_3710, retro_tbel_3722, retro_tbel_3745, retro_tbel_3775, retro_tbel_3780, retro_tbel_3794, retro_tbel_3801, retro_tbel_381, retro_tbel_3812, retro_tbel_3846, retro_tbel_3869, retro_tbel_3873, retro_tbel_398, retro_tbel_3982, retro_tbel_3996, retro_tbel_4033, retro_tbel_4069, retro_tbel_4158, retro_tbel_4161, retro_tbel_4174, retro_tbel_4235, retro_tbel_4247, retro_tbel_4286, retro_tbel_4297, retro_tbel_4363, retro_tbel_4374, retro_tbel_461, retro_tbel_4612, retro_tbel_4646, retro_tbel_466, retro_tbel_488, retro_tbel_503, retro_tbel_510, retro_tbel_577, retro_tbel_599, retro_tbel_626, retro_tbel_696, retro_tbel_718, retro_tbel_741, retro_tbel_744, retro_tbel_780, retro_tbel_788, retro_tbel_872, retro_tbel_886, retro_tbel_891, retro_tbel_908, retro_tbel_914, retro_tbel_942,
Tursiops truncatus	ENSTTRG00000016447	24 retrocopies	retro_ttru_1054, retro_ttru_1072, retro_ttru_1102, retro_ttru_1470, retro_ttru_1717, retro_ttru_215, retro_ttru_230, retro_ttru_262, retro_ttru_281, retro_ttru_316, retro_ttru_40, retro_ttru_482, retro_ttru_507, retro_ttru_527, retro_ttru_67, retro_ttru_671, retro_ttru_690, retro_ttru_785, retro_ttru_80, retro_ttru_804, retro_ttru_842, retro_ttru_886, retro_ttru_896, retro_ttru_99,