RetrogeneDB ID: retro_sscr_1056

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:40464571..40464966(-)
• Located in intron of: ENSSSCG00000021212

Retrocopy information

• Ensembl ID: ENSSSCG00000015006
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS12
• Ensembl ID: ENSSSCG00000004177
• Aliases: None
• Description: Sus scrofa ribosomal protein S12 (RPS12), mRNA. [Source:RefSeq mRNA;Acc:NM_214363]

Sequence

>retro_sscr_1056
ATGGCTAAGGAAGGCATTGCTGCTGCAGGTGTAATGGACATTAATAGTGCTCCACAAGAGGTGCTGAAGACTGCCCTCAT
CCATGATGGCCCAGCACGTGGAATTCTCGAAGCCGCCAAAGCTTTAGACAAGAGCCAAGCCCATCTTTGTGTGCTTGCAT
CCAACTTCGATGAGCCAATGTATGTCAAGGTGGTGGAGGCCCTTTGTGCTGAGCACCAGATCAAACTAATTAAGGTCAAT
AACACAAGAAATGAGGGGAATGGGAAGGCCTCTGTAAAACTGACAGAGAGGGAAAACCCCGTAAAGTGGCCGGTTGTAGT
TGTGTGGTGGTAAAGGACTATTGCAAAGAGTCTCAGGCCAAGGATGTCATCGAGGAGTACTTCAAATGCAAGAAA

Alignment

ORF - retro_sscr_1056 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEEGIAAGGVMDVNTALQEVLKTALIHDGLARGIREAAKALDKRQAHLCVLASNCDEPMYVKLVEALCA
          MA.EGIAA.GVMD.N.A.QEVLKTALIHDG.ARGI.EAAKALDK.QAHLCVLASN.DEPMYVK.VEALCA
Retrocopy MAKEGIAAAGVMDINSAPQEVLKTALIHDGPARGILEAAKALDKSQAHLCVLASNFDEPMYVKVVEALCA

Parental  EHQINLIKVDD-NKKLGEWVGLCKIDREGKPRKVVGCSCVVVKDYGKESQAKDVIEEYFKCKK
          EHQI.LIKV....KK.GEW.GLCK.DREGKPRKV.GCSCVVVKDY.KESQAKDVIEEYFKCKK
Retrocopy EHQIKLIKVNN<HKK*GEWEGLCKTDREGKPRKVAGCSCVVVKDYCKESQAKDVIEEYFKCKK

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	969.73 RPM
SRP014902_testis	0.14 RPM	1077.96 RPM
SRP018288_heart	0.00 RPM	461.35 RPM
SRP018288_kidney	0.00 RPM	416.28 RPM
SRP018288_liver	0.00 RPM	383.30 RPM
SRP018288_lung	0.00 RPM	648.43 RPM
SRP018856_adipose	0.02 RPM	1910.13 RPM
SRP035408_brain	1.18 RPM	514.90 RPM
SRP035408_liver	1.97 RPM	644.98 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1056 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1056 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1056 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 207 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010479	1 retrocopy	retro_acar_102,
Ailuropoda melanoleuca	ENSAMEG00000008015	2 retrocopies	retro_amel_79, retro_amel_92,
Bos taurus	ENSBTAG00000001360	7 retrocopies	retro_btau_106, retro_btau_1097, retro_btau_1306, retro_btau_1495, retro_btau_1514, retro_btau_1630, retro_btau_1802,
Canis familiaris	ENSCAFG00000000190	15 retrocopies	retro_cfam_1033, retro_cfam_1115, retro_cfam_1196, retro_cfam_1280, retro_cfam_1746, retro_cfam_1801, retro_cfam_2026, retro_cfam_2203, retro_cfam_299, retro_cfam_387, retro_cfam_539, retro_cfam_674, retro_cfam_770, retro_cfam_841, retro_cfam_869,
Callithrix jacchus	ENSCJAG00000002865	34 retrocopies	retro_cjac_1038, retro_cjac_1044, retro_cjac_1205, retro_cjac_1291, retro_cjac_1528, retro_cjac_1602, retro_cjac_1778, retro_cjac_1994, retro_cjac_2039, retro_cjac_2058, retro_cjac_2065, retro_cjac_2101, retro_cjac_2112, retro_cjac_2155, retro_cjac_2337, retro_cjac_2406, retro_cjac_2421, retro_cjac_2461, retro_cjac_2681, retro_cjac_2694, retro_cjac_2858, retro_cjac_301, retro_cjac_3310, retro_cjac_4149, retro_cjac_427, retro_cjac_466, retro_cjac_494, retro_cjac_592, retro_cjac_773, retro_cjac_805, retro_cjac_806, retro_cjac_807, retro_cjac_836, retro_cjac_977,
Cavia porcellus	ENSCPOG00000000429	4 retrocopies	retro_cpor_1096, retro_cpor_304, retro_cpor_32, retro_cpor_380,
Equus caballus	ENSECAG00000001599	8 retrocopies	retro_ecab_1012, retro_ecab_1131, retro_ecab_133, retro_ecab_744, retro_ecab_80, retro_ecab_828, retro_ecab_875, retro_ecab_959,
Echinops telfairi	ENSETEG00000006854	14 retrocopies	retro_etel_1129, retro_etel_1512, retro_etel_1580, retro_etel_2016, retro_etel_205, retro_etel_2082, retro_etel_2099, retro_etel_2169, retro_etel_26, retro_etel_280, retro_etel_29, retro_etel_55, retro_etel_578, retro_etel_915,
Felis catus	ENSFCAG00000028402	7 retrocopies	retro_fcat_1084, retro_fcat_1314, retro_fcat_1446, retro_fcat_1880, retro_fcat_537, retro_fcat_664, retro_fcat_796,
Gorilla gorilla	ENSGGOG00000012234	22 retrocopies	retro_ggor_1164, retro_ggor_1287, retro_ggor_1322, retro_ggor_139, retro_ggor_1426, retro_ggor_1441, retro_ggor_1686, retro_ggor_1861, retro_ggor_1894, retro_ggor_2115, retro_ggor_2241, retro_ggor_2261, retro_ggor_2339, retro_ggor_2456, retro_ggor_2489, retro_ggor_2680, retro_ggor_3076, retro_ggor_530, retro_ggor_595, retro_ggor_673, retro_ggor_724, retro_ggor_971,
Gadus morhua	ENSGMOG00000019455	1 retrocopy	retro_gmor_11,
Microcebus murinus	ENSMICG00000005252	5 retrocopies	retro_mmur_1260, retro_mmur_1527, retro_mmur_391, retro_mmur_491, retro_mmur_98,
Myotis lucifugus	ENSMLUG00000001137	5 retrocopies	retro_mluc_1479, retro_mluc_1552, retro_mluc_1987, retro_mluc_1988, retro_mluc_582,
Macaca mulatta	ENSMMUG00000013237	1 retrocopy	retro_mmul_12,
Mustela putorius furo	ENSMPUG00000014771	1 retrocopy	retro_mputfur_6,
Mus musculus	ENSMUSG00000061983	1 retrocopy	retro_mmus_36,
Nomascus leucogenys	ENSNLEG00000014611	4 retrocopies	retro_nleu_2717, retro_nleu_543, retro_nleu_588, retro_nleu_86,
Pongo abelii	ENSPPYG00000017020	26 retrocopies	retro_pabe_1032, retro_pabe_1044, retro_pabe_1266, retro_pabe_1441, retro_pabe_1475, retro_pabe_1619, retro_pabe_1621, retro_pabe_1952, retro_pabe_1961, retro_pabe_2213, retro_pabe_2551, retro_pabe_2694, retro_pabe_2757, retro_pabe_2863, retro_pabe_2987, retro_pabe_3017, retro_pabe_3280, retro_pabe_3473, retro_pabe_526, retro_pabe_582, retro_pabe_591, retro_pabe_641, retro_pabe_654, retro_pabe_704, retro_pabe_773, retro_pabe_888,
Pelodiscus sinensis	ENSPSIG00000003457	1 retrocopy	retro_psin_52,
Rattus norvegicus	ENSRNOG00000016411	5 retrocopies	retro_rnor_177, retro_rnor_186, retro_rnor_241, retro_rnor_295, retro_rnor_300,
Sorex araneus	ENSSARG00000003170	2 retrocopies	retro_sara_356, retro_sara_8,
Sarcophilus harrisii	ENSSHAG00000008905	6 retrocopies	retro_shar_187, retro_shar_226, retro_shar_475, retro_shar_492, retro_shar_621, retro_shar_671,
Sus scrofa	ENSSSCG00000004177	8 retrocopies	retro_sscr_1056 , retro_sscr_1100, retro_sscr_1216, retro_sscr_125, retro_sscr_382, retro_sscr_663, retro_sscr_790, retro_sscr_875,
Tarsius syrichta	ENSTSYG00000010097	24 retrocopies	retro_tsyr_1010, retro_tsyr_102, retro_tsyr_1123, retro_tsyr_1188, retro_tsyr_129, retro_tsyr_1313, retro_tsyr_1345, retro_tsyr_1398, retro_tsyr_1486, retro_tsyr_1668, retro_tsyr_1955, retro_tsyr_1993, retro_tsyr_205, retro_tsyr_249, retro_tsyr_303, retro_tsyr_419, retro_tsyr_453, retro_tsyr_556, retro_tsyr_645, retro_tsyr_733, retro_tsyr_764, retro_tsyr_801, retro_tsyr_970, retro_tsyr_99,
Vicugna pacos	ENSVPAG00000011504	3 retrocopies	retro_vpac_133, retro_vpac_267, retro_vpac_339,