RetrogeneDB ID: retro_hsap_588

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:70434105..70434668(+)
• Located in intron of: ENSG00000138336

Retrocopy information

• Ensembl ID: ENSG00000227583
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS3A
• Ensembl ID: ENSG00000145425
• Aliases: RPS3A, FTE1, MFTL, S3A
• Description: ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]

Sequence

>retro_hsap_588
GGCAGCACAAAGGGAGCCAAGAAGAAAGTGCTTGATCCATTTTCTAAGAAAGATTTGTATTACGTGAAAGCATCTGCCAT
GTTCAATATAAGAAATATTGGGAAGACACTAGTCACCAGAACCCAAGGAACCATAATTGAATCTGATGGCCTCAAGGGTC
GTGTATTTGAAGTGAGTCTTGCTGATATGCAGAATGATAAAGTTGCATTTAGAAAATTCAGCTGATTACTGAAGATGTTC
AGGGGAATGATTGCCTGATGAGCTTCCATGGCGTGGATCTTACCTGTGACAAAATATGTTTCATGGTCAAAAAATGGCAG
ACAATGGTTGAAGGTCATGTCAATATCAAGACTACCGGTGCTTACTTGCTTCATGTGTTCTGTGTTGGTTTTACTAAAAA
ATGCAACAATCAGATACGGAAGACCTCTTATGCTTAGCACCAATGTTTCGGCCAAATCTGGAACAAGTTGATGGAAATCA
TGACCCGAGAGGTGCAGACAAATTACTTGAAAGAAGTGGTCAATAAATTGATTCCAGACAGGATTGGAAAAGACATAGAA
AAA

Alignment

ORF - retro_hsap_588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.89 %
• Parental protein coverage: 71.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAF
          G..KGAKKKV.DPFSKKD.Y.VKA.AMFNIRNIGKTLVTRTQGT.I.SDGLKGRVFEVSLAD.QND.VAF
Retrocopy GSTKGAKKKVLDPFSKKDLYYVKASAMFNIRNIGKTLVTRTQGTIIESDGLKGRVFEVSLADMQNDKVAF

Parental  RKF-KLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQI
          RKF..LITEDVQG..CL..FHG.DLT.DK.C.MVKKWQTM.E.HV..KTT..YLL..FCVGFTKK.NNQI
Retrocopy RKF<QLITEDVQGNDCLMSFHGVDLTCDKICFMVKKWQTMVEGHVNIKTTGAYLLHVFCVGFTKKCNNQI

Parental  RKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEK
          RKTSYA.HQ...QI..K.MEIMTREVQTN.LKEVVNKLIPD.IGKDIEK
Retrocopy RKTSYA*HQCFGQIWNKLMEIMTREVQTNYLKEVVNKLIPDRIGKDIEK

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
bodymap2_adipose	0.00 RPM	165.82 RPM
bodymap2_adrenal	0.04 RPM	364.03 RPM
bodymap2_brain	0.07 RPM	75.31 RPM
bodymap2_breast	0.04 RPM	171.42 RPM
bodymap2_colon	0.00 RPM	412.69 RPM
bodymap2_heart	0.00 RPM	106.78 RPM
bodymap2_kidney	0.00 RPM	159.90 RPM
bodymap2_liver	0.00 RPM	109.78 RPM
bodymap2_lung	0.00 RPM	488.03 RPM
bodymap2_lymph_node	0.05 RPM	443.21 RPM
bodymap2_ovary	0.00 RPM	526.47 RPM
bodymap2_prostate	0.00 RPM	540.27 RPM
bodymap2_skeletal_muscle	0.00 RPM	86.34 RPM
bodymap2_testis	0.04 RPM	259.98 RPM
bodymap2_thyroid	0.00 RPM	233.87 RPM
bodymap2_white_blood_cells	0.00 RPM	665.11 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_588 was not detected

EST

No EST(s) were mapped for retro_hsap_588 retrocopy.

TSS

No TSS is located nearby retro_hsap_588 retrocopy 5' end.

Lab

retro_hsap_588 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_588 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_602

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 197 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,
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,