RetrogeneDB ID: retro_sscr_136

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:207458810..207459375(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000029467
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS7
• Ensembl ID: ENSSSCG00000027353
• Aliases: None
• Description: ribosomal protein S7 [Source:HGNC Symbol;Acc:10440]

Sequence

>retro_sscr_136
TCCAGGACAAAGATCGTGAAGCCCAATGGCGAGAAGCCGGACGAGTTAAAGTCGGCATCTCCCAGGCCCTCCTGGAGCTG
GAGATGAACTCGGACCTCAAGGCCCAGCTGCGCAAGCTGAACATCACGGCCACCAAGAAAATCAAAGTGGGCAGCGGTCG
GAAAGCCATCATCATCTTTGTGCCGGTTCCCCAACTGAAGTCTTTCCAGAAGATCCAGGTGCGGCTCGTGCACGAGCTGG
AGAAGAAGTTCAGCGGGAAGCACGTGGTCTTCATCGCTCAGAGGAGAATTCTGCCTAAGCCAACTCGAAAAAGCCGTACA
AAAAATAAGCAGAAGCGTCCCAGAAGCCGCACCCTGATAGCTGTGCACGATGCCATCCTGGAGGACCTGGTTTTCCCAAG
TGAGATTGTGGGCAAGAGAATCCGCCTGAAGCTGGATGGCAGCCACTCTTCAAGGTCCATTTGGACAAAGCACAGCAGAA
CTACGTGGAGCACAACATTGAAACATTTTCTGGTGTCTATAAGAAGCTCACGGGCAAGGACATTAATTTTGAATTCCCAG
AGTTT

Alignment

ORF - retro_sscr_136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.53 %
• Parental protein coverage: 97.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSAKIVKPNGEKPDEFES-GISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLKSF
          S..KIVKPNGEKPDE..S.GISQALLELEMNSDLKAQLR.LNITA.K.I.VG.GRKAIIIFVPVPQLKSF
Retrocopy SRTKIVKPNGEKPDELKS<GISQALLELEMNSDLKAQLRKLNITATKKIKVGSGRKAIIIFVPVPQLKSF

Parental  QKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIVGK
          QKIQVRLV.ELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTL.AVHDAILEDLVFPSEIVGK
Retrocopy QKIQVRLVHELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLIAVHDAILEDLVFPSEIVGK

Parental  RIRVKLDGSR-LIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEF
          RIR.KLDGS..L.KVHLDKAQQN.VEH..ETFSGVYKKLTGKD.NFEFPEF
Retrocopy RIRLKLDGSH<LFKVHLDKAQQNYVEHNIETFSGVYKKLTGKDINFEFPEF

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	595.70 RPM
SRP014902_testis	0.00 RPM	1672.18 RPM
SRP018288_heart	0.00 RPM	389.26 RPM
SRP018288_kidney	0.00 RPM	502.67 RPM
SRP018288_liver	0.00 RPM	405.85 RPM
SRP018288_lung	0.00 RPM	760.34 RPM
SRP018856_adipose	0.00 RPM	801.54 RPM
SRP035408_brain	0.00 RPM	613.80 RPM
SRP035408_liver	0.00 RPM	805.64 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_136 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_136 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 89 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018435	2 retrocopies	retro_amel_391, retro_amel_914,
Callithrix jacchus	ENSCJAG00000016462	2 retrocopies	retro_cjac_16, retro_cjac_2287,
Dasypus novemcinctus	ENSDNOG00000013285	14 retrocopies	retro_dnov_1091, retro_dnov_1351, retro_dnov_1388, retro_dnov_1459, retro_dnov_1688, retro_dnov_1849, retro_dnov_1940, retro_dnov_1970, retro_dnov_238, retro_dnov_2409, retro_dnov_558, retro_dnov_582, retro_dnov_623, retro_dnov_791,
Equus caballus	ENSECAG00000020253	2 retrocopies	retro_ecab_276, retro_ecab_396,
Felis catus	ENSFCAG00000023243	2 retrocopies	retro_fcat_1534, retro_fcat_41,
Gorilla gorilla	ENSGGOG00000023095	13 retrocopies	retro_ggor_2028, retro_ggor_2090, retro_ggor_2161, retro_ggor_218, retro_ggor_2452, retro_ggor_2927, retro_ggor_294, retro_ggor_2965, retro_ggor_3047, retro_ggor_346, retro_ggor_400, retro_ggor_484, retro_ggor_597,
Loxodonta africana	ENSLAFG00000015087	11 retrocopies	retro_lafr_1223, retro_lafr_160, retro_lafr_217, retro_lafr_318, retro_lafr_319, retro_lafr_413, retro_lafr_514, retro_lafr_720, retro_lafr_786, retro_lafr_964, retro_lafr_970,
Myotis lucifugus	ENSMLUG00000006121	1 retrocopy	retro_mluc_1118,
Macaca mulatta	ENSMMUG00000011870	7 retrocopies	retro_mmul_1831, retro_mmul_1846, retro_mmul_1929, retro_mmul_23, retro_mmul_2403, retro_mmul_2540, retro_mmul_357,
Nomascus leucogenys	ENSNLEG00000015407	10 retrocopies	retro_nleu_1505, retro_nleu_1771, retro_nleu_1783, retro_nleu_2278, retro_nleu_2346, retro_nleu_2510, retro_nleu_2892, retro_nleu_3080, retro_nleu_817, retro_nleu_835,
Otolemur garnettii	ENSOGAG00000028165	1 retrocopy	retro_ogar_133,
Pan troglodytes	ENSPTRG00000011615	3 retrocopies	retro_ptro_202, retro_ptro_3132, retro_ptro_58,
Pteropus vampyrus	ENSPVAG00000002071	7 retrocopies	retro_pvam_1051, retro_pvam_1183, retro_pvam_1330, retro_pvam_1437, retro_pvam_207, retro_pvam_543, retro_pvam_887,
Sus scrofa	ENSSSCG00000027353	5 retrocopies	retro_sscr_136 , retro_sscr_137, retro_sscr_240, retro_sscr_364, retro_sscr_956,
Ictidomys tridecemlineatus	ENSSTOG00000024830	3 retrocopies	retro_itri_1147, retro_itri_1161, retro_itri_1215,
Tursiops truncatus	ENSTTRG00000001616	6 retrocopies	retro_ttru_1422, retro_ttru_1659, retro_ttru_1706, retro_ttru_301, retro_ttru_323, retro_ttru_773,