RetrogeneDB ID: retro_sscr_27

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:81602251..81603007(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000002045
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPS3A
• Ensembl ID: ENSSSCG00000009019
• Aliases: None
• Description: ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]

Sequence

>retro_sscr_27
ATGGCGGTTGGCAAGAATAAGTGCCTTACGAAAGGCGGCAAAAAGGGAGCCAAGAAGAAAGTGGTTGACCCATTTTCTAA
GAAAGATTGGTATGATGTGAAAGCACCAGCTATGTTCAATATAAGAAATATTGGGAAAACACTGGTCACAAGAACTCAAG
GAACCAAAGTTGCATCTGACAGCCTCAAGGGTCGTGTGTTTGAAGTGAGCCTTGCCTATCTGCAGAACGATGAAGTTGCA
TTTAGAAAATTCAAGCTGATTACTGAGGATGTTCAGGGCAAAAACTGCTTGACCACTTTCCACGGCATGGATCTTACCCA
TGACAAGATGTGCTCAATGGTCAAAAAACGGCAGACCATGATTGAAGCTCACGTTGATGTCAAGACTACCGATGGTTATT
TGCTTCGTCTGTTCTGTGTTGGTTTTACTAAAAAATGCAACAATCAGATTCGGAAGACCTCTTACACCCAGCACCAACAA
GTCTGCCAAATCCAGAAGAAGATGATGGAAATCATGACACGAGAGGTGCAGACAAATGACTTGAAAGAGGTGGTCAATAA
ATTGATTCAAGACAGCATTGGAAAGGACATAGAAAAGGCTTGCCAATCTATTTATCTGCTTCATGACGTCTTCGTTGGAA
AAGTAAAAATGCTGAAGAAGCCCAAGTTTGAATTGGGAAAACTCATGGAGCTACATGGTGAAGGTAGTAGTTCTGGAAAA
GCTACTGGGGATGAGACAGGTGCTAAAGTTGAATGA

Alignment

ORF - retro_sscr_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.42 %
• Parental protein coverage: 95.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVS
          MAVGKNK.LTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTK.ASD.LKGRVFEVS
Retrocopy MAVGKNKCLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKVASDSLKGRVFEVS

Parental  LADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
          LA.LQNDEVAFRKFKLITEDVQGKNCLT.FHGMDLT.DKMCSMVKK.QTMIEAHVDVKTTDGYLLRLFCV
Retrocopy LAYLQNDEVAFRKFKLITEDVQGKNCLTTFHGMDLTHDKMCSMVKKRQTMIEAHVDVKTTDGYLLRLFCV

Parental  GFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDV
          GFTKK.NNQIRKTSY.QHQQV.QI.KKMMEIMTREVQTNDLKEVVNKLI.DSIGKDIEKACQSIY.LHDV
Retrocopy GFTKKCNNQIRKTSYTQHQQVCQIQKKMMEIMTREVQTNDLKEVVNKLIQDSIGKDIEKACQSIYLLHDV

Parental  FVRKVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVE
          FV.KVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVE
Retrocopy FVGKVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVE

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	0.13 RPM	281.66 RPM
SRP014902_testis	2.97 RPM	599.31 RPM
SRP018288_heart	0.89 RPM	789.40 RPM
SRP018288_kidney	1.28 RPM	593.30 RPM
SRP018288_liver	4.00 RPM	512.99 RPM
SRP018288_lung	3.87 RPM	537.03 RPM
SRP018856_adipose	0.92 RPM	1162.09 RPM
SRP035408_brain	0.44 RPM	575.50 RPM
SRP035408_liver	0.26 RPM	488.04 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_27 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_27 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_27 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 211 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002268	7 retrocopies	retro_cjac_2, retro_cjac_21, retro_cjac_249, retro_cjac_312, retro_cjac_337, retro_cjac_368, retro_cjac_78,
Dipodomys ordii	ENSDORG00000002250	10 retrocopies	retro_dord_142, retro_dord_168, retro_dord_193, retro_dord_209, retro_dord_229, retro_dord_314, retro_dord_380, retro_dord_752, retro_dord_757, retro_dord_95,
Erinaceus europaeus	ENSEEUG00000004994	4 retrocopies	retro_eeur_297, retro_eeur_510, retro_eeur_517, retro_eeur_66,
Homo sapiens	ENSG00000145425	40 retrocopies	retro_hsap_1080, retro_hsap_1178, retro_hsap_1320, retro_hsap_144, retro_hsap_1507, retro_hsap_1559, retro_hsap_1620, retro_hsap_1891, retro_hsap_1994, retro_hsap_2575, retro_hsap_2578, retro_hsap_2607, retro_hsap_2700, retro_hsap_274, retro_hsap_2803, retro_hsap_2908, retro_hsap_2909, retro_hsap_3020, retro_hsap_3112, retro_hsap_313, retro_hsap_3213, retro_hsap_3366, retro_hsap_3675, retro_hsap_3876, retro_hsap_3878, retro_hsap_3879, retro_hsap_3910, retro_hsap_3929, retro_hsap_3931, retro_hsap_4017, retro_hsap_4020, retro_hsap_4021, retro_hsap_588, retro_hsap_602, retro_hsap_613, retro_hsap_683, retro_hsap_789, retro_hsap_838, retro_hsap_888, retro_hsap_914,
Gorilla gorilla	ENSGGOG00000003182	2 retrocopies	retro_ggor_70, retro_ggor_97,
Myotis lucifugus	ENSMLUG00000014788	8 retrocopies	retro_mluc_1197, retro_mluc_1397, retro_mluc_1568, retro_mluc_1846, retro_mluc_2130, retro_mluc_2158, retro_mluc_2388, retro_mluc_862,
Macaca mulatta	ENSMMUG00000021821	1 retrocopy	retro_mmul_2297,
Monodelphis domestica	ENSMODG00000000969	6 retrocopies	retro_mdom_1040, retro_mdom_1229, retro_mdom_1396, retro_mdom_1480, retro_mdom_627, retro_mdom_694,
Mus musculus	ENSMUSG00000028081	2 retrocopies	retro_mmus_218, retro_mmus_254,
Nomascus leucogenys	ENSNLEG00000005815	26 retrocopies	retro_nleu_1160, retro_nleu_1177, retro_nleu_1402, retro_nleu_1472, retro_nleu_1483, retro_nleu_1487, retro_nleu_1816, retro_nleu_1878, retro_nleu_1992, retro_nleu_209, retro_nleu_2437, retro_nleu_2567, retro_nleu_2571, retro_nleu_2753, retro_nleu_281, retro_nleu_2979, retro_nleu_3087, retro_nleu_443, retro_nleu_526, retro_nleu_654, retro_nleu_658, retro_nleu_758, retro_nleu_767, retro_nleu_799, retro_nleu_942, retro_nleu_962,
Oryctolagus cuniculus	ENSOCUG00000007011	1 retrocopy	retro_ocun_257,
Rattus norvegicus	ENSRNOG00000011893	1 retrocopy	retro_rnor_198,
Sarcophilus harrisii	ENSSHAG00000015088	2 retrocopies	retro_shar_777, retro_shar_95,
Sus scrofa	ENSSSCG00000009019	3 retrocopies	retro_sscr_27 , retro_sscr_749, retro_sscr_762,
Tupaia belangeri	ENSTBEG00000002963	98 retrocopies	retro_tbel_1005, retro_tbel_11, retro_tbel_1119, retro_tbel_116, retro_tbel_1232, retro_tbel_1318, retro_tbel_133, retro_tbel_137, retro_tbel_1375, retro_tbel_1378, retro_tbel_1383, retro_tbel_1417, retro_tbel_1421, retro_tbel_1509, retro_tbel_1686, retro_tbel_1698, retro_tbel_172, retro_tbel_1720, retro_tbel_1721, retro_tbel_1744, retro_tbel_1814, retro_tbel_1829, retro_tbel_1856, retro_tbel_1896, retro_tbel_1948, retro_tbel_1960, retro_tbel_1999, retro_tbel_206, retro_tbel_2200, retro_tbel_2306, retro_tbel_2463, retro_tbel_2483, retro_tbel_2510, retro_tbel_2626, retro_tbel_2654, retro_tbel_2657, retro_tbel_2745, retro_tbel_2759, retro_tbel_2760, retro_tbel_2764, retro_tbel_281, retro_tbel_2857, retro_tbel_2957, retro_tbel_2959, retro_tbel_3114, retro_tbel_317, retro_tbel_3212, retro_tbel_3255, retro_tbel_3259, retro_tbel_3299, retro_tbel_336, retro_tbel_3372, retro_tbel_3416, retro_tbel_3471, retro_tbel_3486, retro_tbel_3513, retro_tbel_3558, retro_tbel_3613, retro_tbel_3631, retro_tbel_3655, retro_tbel_3705, retro_tbel_373, retro_tbel_375, retro_tbel_3755, retro_tbel_3786, retro_tbel_3815, retro_tbel_3823, retro_tbel_3832, retro_tbel_386, retro_tbel_3882, retro_tbel_39, retro_tbel_3947, retro_tbel_3966, retro_tbel_399, retro_tbel_4116, retro_tbel_4144, retro_tbel_4147, retro_tbel_4211, retro_tbel_4220, retro_tbel_423, retro_tbel_4294, retro_tbel_4304, retro_tbel_4347, retro_tbel_438, retro_tbel_4428, retro_tbel_445, retro_tbel_4579, retro_tbel_598, retro_tbel_619, retro_tbel_623, retro_tbel_671, retro_tbel_859, retro_tbel_90, retro_tbel_912, retro_tbel_92, retro_tbel_928, retro_tbel_956, retro_tbel_973,