RetrogeneDB ID: retro_sscr_290

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 12:5953073..5953581(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL13A
• Ensembl ID: ENSSSCG00000003166
• Aliases: None
• Description: Sus scrofa ribosomal protein L13a (RPL13A), transcript variant 1, mRNA. [Source:RefSeq mRNA;Acc:NM_001244068]

Sequence

>retro_sscr_290
ATGGGAGAGGGGCAGCAGGTGCTTCTGCTCCACGGCCAAGGCCACCTCCTGGACTACCTGGAGGCCATGGTTGCCGAGCA
GGTGCTTCTGGGCCAGAAGGGGGTGGTTGTGTGCTATGAGGGCATCAACATTTCTGGCAATTTCTACAGAAACAAACGGA
AGTACCTAGTCTTCCTCCGCAAGCGGGTGCGCACCAACCCATCCCGCGGCTCCAACCACTTCTGAGCCCCAAGCCACATC
CGCTGGTGGGTGGCGCAGGGCTTGCTGCCCCACAAGACCCAGCCTGGCCAGGCCACCCCGGAACCCTCGGATGGTGTTTT
AGGGGGCCCTGCCGCCCTATGACAAGAAAAAGGGGATCGTGGGTCCTGCCGCCCTCAAAATGGTGCACCTGAAGCCTACA
GGGAAGTTTGCCTACCTGGCTCATGAGGTTGCCTGGAAGTACCAGGCAGTAACCACCACCCTGGAGAAGAGGAAGGAGAA
CGCCAAGATCCATTACTGCAAGAAGAGG

Alignment

ORF - retro_sscr_290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.39 %
• Parental protein coverage: 84.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEGQQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPSRG
          M.EGQQVL.L.G.GHLL..L.A.VA.QVLLG.K.VVV..EGINISGNFYRNK.KYL.FLRKR..TNPSRG
Retrocopy MGEGQQVLLLHGQGHLLDYLEAMVAEQVLLGQKGVVVCYEGINISGNFYRNKRKYLVFLRKRVRTNPSRG

Parental  PYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIP-PPYDKKKRMVVPAALKVVRLKPTRKFAYL
          ..HF.APS.I.W....G.LPHKT..GQA.........G.P.PPYDKKK..V.PAALK.V.LKPT.KFAYL
Retrocopy SNHF*APSHIRWWVAQGLLPHKTQPGQATPEPSDGVLGGP>PPYDKKKGIVGPAALKMVHLKPTGKFAYL

Parental  GRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKK
          ...AHEV.WKYQAVT.TL.EKRKE.AKIHY.KK.
Retrocopy ---AHEVAWKYQAVTTTL-EKRKENAKIHYCKKR

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	596.49 RPM
SRP014902_testis	0.00 RPM	1096.35 RPM
SRP018288_heart	0.00 RPM	331.72 RPM
SRP018288_kidney	0.00 RPM	375.31 RPM
SRP018288_liver	0.00 RPM	253.62 RPM
SRP018288_lung	0.00 RPM	443.45 RPM
SRP018856_adipose	0.00 RPM	599.82 RPM
SRP035408_brain	0.00 RPM	1828.74 RPM
SRP035408_liver	0.00 RPM	1076.01 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_290 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_290 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 30 parental genes, and 192 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014027	2 retrocopies	retro_amel_1332, retro_amel_1720,
Bos taurus	ENSBTAG00000005296	3 retrocopies	retro_btau_1251, retro_btau_719, retro_btau_789,
Canis familiaris	ENSCAFG00000029892	3 retrocopies	retro_cfam_1772, retro_cfam_924, retro_cfam_976,
Callithrix jacchus	ENSCJAG00000000072	16 retrocopies	retro_cjac_1130, retro_cjac_1706, retro_cjac_182, retro_cjac_197, retro_cjac_1997, retro_cjac_2170, retro_cjac_2322, retro_cjac_2467, retro_cjac_2468, retro_cjac_2665, retro_cjac_2699, retro_cjac_2755, retro_cjac_3009, retro_cjac_664, retro_cjac_941, retro_cjac_972,
Cavia porcellus	ENSCPOG00000012417	2 retrocopies	retro_cpor_1000, retro_cpor_888,
Equus caballus	ENSECAG00000015832	3 retrocopies	retro_ecab_388, retro_ecab_653, retro_ecab_773,
Erinaceus europaeus	ENSEEUG00000014071	6 retrocopies	retro_eeur_168, retro_eeur_310, retro_eeur_315, retro_eeur_484, retro_eeur_562, retro_eeur_618,
Echinops telfairi	ENSETEG00000017076	2 retrocopies	retro_etel_46, retro_etel_853,
Felis catus	ENSFCAG00000009194	4 retrocopies	retro_fcat_1197, retro_fcat_1649, retro_fcat_324, retro_fcat_548,
Homo sapiens	ENSG00000142541	22 retrocopies	retro_hsap_1072, retro_hsap_1100, retro_hsap_1111, retro_hsap_1268, retro_hsap_1410, retro_hsap_2200, retro_hsap_2500, retro_hsap_293, retro_hsap_298, retro_hsap_3173, retro_hsap_3350, retro_hsap_3444, retro_hsap_3652, retro_hsap_3752, retro_hsap_3772, retro_hsap_397, retro_hsap_436, retro_hsap_615, retro_hsap_671, retro_hsap_730, retro_hsap_753, retro_hsap_967,
Gorilla gorilla	ENSGGOG00000002932	11 retrocopies	retro_ggor_12, retro_ggor_1739, retro_ggor_214, retro_ggor_2271, retro_ggor_2737, retro_ggor_334, retro_ggor_6, retro_ggor_615, retro_ggor_627, retro_ggor_846, retro_ggor_869,
Loxodonta africana	ENSLAFG00000016213	3 retrocopies	retro_lafr_1160, retro_lafr_576, retro_lafr_810,
Microcebus murinus	ENSMICG00000009318	6 retrocopies	retro_mmur_240, retro_mmur_283, retro_mmur_311, retro_mmur_359, retro_mmur_65, retro_mmur_736,
Myotis lucifugus	ENSMLUG00000004945	10 retrocopies	retro_mluc_1015, retro_mluc_1342, retro_mluc_1836, retro_mluc_1894, retro_mluc_2219, retro_mluc_2221, retro_mluc_2427, retro_mluc_2471, retro_mluc_2506, retro_mluc_675,
Macaca mulatta	ENSMMUG00000007551	14 retrocopies	retro_mmul_1100, retro_mmul_1256, retro_mmul_1638, retro_mmul_1756, retro_mmul_2179, retro_mmul_2249, retro_mmul_2352, retro_mmul_2399, retro_mmul_296, retro_mmul_500, retro_mmul_520, retro_mmul_547, retro_mmul_837, retro_mmul_924,
Mustela putorius furo	ENSMPUG00000002604	3 retrocopies	retro_mputfur_1418, retro_mputfur_853, retro_mputfur_935,
Mus musculus	ENSMUSG00000074129	3 retrocopies	retro_mmus_1129, retro_mmus_1334, retro_mmus_20,
Nomascus leucogenys	ENSNLEG00000005211	23 retrocopies	retro_nleu_1173, retro_nleu_1429, retro_nleu_1568, retro_nleu_159, retro_nleu_1823, retro_nleu_1873, retro_nleu_1892, retro_nleu_1897, retro_nleu_2047, retro_nleu_228, retro_nleu_2398, retro_nleu_2415, retro_nleu_2463, retro_nleu_2614, retro_nleu_2789, retro_nleu_2928, retro_nleu_330, retro_nleu_392, retro_nleu_441, retro_nleu_475, retro_nleu_513, retro_nleu_744, retro_nleu_760,
Oryctolagus cuniculus	ENSOCUG00000025258	9 retrocopies	retro_ocun_1038, retro_ocun_1077, retro_ocun_1392, retro_ocun_1462, retro_ocun_304, retro_ocun_674, retro_ocun_756, retro_ocun_786, retro_ocun_972,
Otolemur garnettii	ENSOGAG00000004625	7 retrocopies	retro_ogar_1496, retro_ogar_211, retro_ogar_2254, retro_ogar_3148, retro_ogar_54, retro_ogar_596, retro_ogar_612,
Ochotona princeps	ENSOPRG00000001194	3 retrocopies	retro_opri_316, retro_opri_764, retro_opri_806,
Procavia capensis	ENSPCAG00000004086	4 retrocopies	retro_pcap_163, retro_pcap_290, retro_pcap_415, retro_pcap_416,
Pongo abelii	ENSPPYG00000010251	1 retrocopy	retro_pabe_148,
Pan troglodytes	ENSPTRG00000011298	1 retrocopy	retro_ptro_31,
Pteropus vampyrus	ENSPVAG00000010958	3 retrocopies	retro_pvam_129, retro_pvam_625, retro_pvam_771,
Rattus norvegicus	ENSRNOG00000020618	10 retrocopies	retro_rnor_1073, retro_rnor_1112, retro_rnor_1212, retro_rnor_1292, retro_rnor_1357, retro_rnor_1742, retro_rnor_564, retro_rnor_593, retro_rnor_665, retro_rnor_988,
Sus scrofa	ENSSSCG00000003166	4 retrocopies	retro_sscr_290 , retro_sscr_300, retro_sscr_392, retro_sscr_743,
Tupaia belangeri	ENSTBEG00000016579	3 retrocopies	retro_tbel_2417, retro_tbel_4071, retro_tbel_958,
Tarsius syrichta	ENSTSYG00000008791	4 retrocopies	retro_tsyr_1363, retro_tsyr_437, retro_tsyr_620, retro_tsyr_920,
Tursiops truncatus	ENSTTRG00000005485	7 retrocopies	retro_ttru_1304, retro_ttru_1736, retro_ttru_629, retro_ttru_735, retro_ttru_833, retro_ttru_971, retro_ttru_995,