RetrogeneDB ID: retro_hsap_1688

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 16:48611437..48612198(-)
• Located in intron of: ENSG00000102921

Retrocopy information

• Ensembl ID: ENSG00000243609
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS2
• Ensembl ID: ENSG00000140988
• Aliases: RPS2, LLREP3, S2
• Description: ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]

Sequence

>retro_hsap_1688
GGATGAGGAACTGCAGAGGCTTCCGCATTGGCATCTGGGGCTAGGGCCTCAGCCAAGGACAAGAAATATATGCCCATTAC
CAAGCTGGGCCACCTGGTCAAGAACATGAAGATCAAGTCCCTGGAGGAAATCCATCTCTTCTCCCTGCCCATCAAGGAGT
CTAAGATCATTGACTTTTAACTGGGGGCTCTCTCAAGGATGAGGTTTTGAAGATTATGCCAATGCAGAAGCACACGTGCA
TCAGCCAGCACATCAGGTTCAAGGCATTTGTTGCCTTCAGGGACTAGAACGGTCACGTCTAGTGTGGGTGTTAAGTGTTC
CAAGGAGATGCCGTCCGAGGGGCCATCATTCTGGCCAAGCTTTTCATTGTTCCCGTGCACAGAGGTTACTGGGGGAACAA
GATCAGCAAGCCCCACACCATCCCTTGCAAGGTGACAGGCCACTGCAGCTCTGTGCTTGTGCGCCTCATCCCTGCGCCCA
GGGGCACTGGTGTCATCTCGGCCCCGGTACCCAAGAAGCTGCTGCTGGTGGCTGGTATTGATGATTGCTACACCTCAGCC
AGGAGCTGCACTGCCACCCTGGGCAACTTTGCCAAGACCACCTTTGATGCCATCTCCAAGACCTACAGCTGCCTGACCCC
CGACCTCTGGAAGAAGACTGTGTTCACCAAGTCTCCCTATGAGGAATTCACTGACCACCTCGTCAAGACCCACACCAGAG
TCTCCATGCAAAGGACCCAGGCTGCAGCTGTGGCTGCAACA

Alignment

ORF - retro_hsap_1688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.97 %
• Parental protein coverage: 87.71 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRGRGRGRGRGRGARGGKAEDKEWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGA-SLKDE
          G.G.........GAR...A.DK..MP.TKLG.LVK.MKIKSLEEI.LFSLPIKES.IIDF.LGA.SLKDE
Retrocopy G*GTAEASALASGARAS-AKDKKYMPITKLGHLVKNMKIKSLEEIHLFSLPIKESKIIDF*LGA<SLKDE

Parental  VLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIG
          VLKIMP.QK.T...Q..RFKAFVA..D.NGHV..G..C......A.RGAIILAKL.IVPV.RGYWGNKI.
Retrocopy VLKIMPMQKHTCISQHIRFKAFVAFRD*NGHV*CG--C*VFQGDAVRGAIILAKLFIVPVHRGYWGNKIS

Parental  KPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAIS
          KPHT.PCKVTG.C.SVLVRLIPAPRGTG..SAPVPKKLL..AGIDDCYTSAR.CTATLGNFAK.TFDAIS
Retrocopy KPHTIPCKVTGHCSSVLVRLIPAPRGTGVISAPVPKKLLLVAGIDDCYTSARSCTATLGNFAKTTFDAIS

Parental  KTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT
          KTYS.LTPDLWK.TVFTKSPY.EFTDHLVKTHTRVS.QRTQA.AVA.T
Retrocopy KTYSCLTPDLWKKTVFTKSPYEEFTDHLVKTHTRVSMQRTQAAAVAAT

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	0.02 RPM	496.47 RPM
bodymap2_adrenal	0.14 RPM	505.10 RPM
bodymap2_brain	0.02 RPM	53.79 RPM
bodymap2_breast	0.00 RPM	261.89 RPM
bodymap2_colon	0.00 RPM	444.16 RPM
bodymap2_heart	0.02 RPM	116.21 RPM
bodymap2_kidney	0.06 RPM	179.65 RPM
bodymap2_liver	0.00 RPM	249.89 RPM
bodymap2_lung	0.00 RPM	464.79 RPM
bodymap2_lymph_node	0.00 RPM	651.42 RPM
bodymap2_ovary	0.00 RPM	445.62 RPM
bodymap2_prostate	0.00 RPM	603.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	731.68 RPM
bodymap2_testis	0.00 RPM	238.89 RPM
bodymap2_thyroid	0.00 RPM	257.52 RPM
bodymap2_white_blood_cells	0.02 RPM	782.33 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1688 was not detected

EST

No EST(s) were mapped for retro_hsap_1688 retrocopy.

TSS

No TSS is located nearby retro_hsap_1688 retrocopy 5' end.

Lab

retro_hsap_1688 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1688 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Felis catus	ENSFCAG00000029191	6 retrocopies	retro_fcat_1245, retro_fcat_1328, retro_fcat_1606, retro_fcat_1610, retro_fcat_1737, retro_fcat_517,
Homo sapiens	ENSG00000140988	47 retrocopies	retro_hsap_1060, retro_hsap_136, retro_hsap_140, retro_hsap_141, retro_hsap_1443, retro_hsap_1444, retro_hsap_1457, retro_hsap_1463, retro_hsap_148, retro_hsap_1648, retro_hsap_1688 , retro_hsap_1722, retro_hsap_1812, retro_hsap_1830, retro_hsap_1831, retro_hsap_1838, retro_hsap_1845, retro_hsap_1897, retro_hsap_1953, retro_hsap_1965, retro_hsap_1971, retro_hsap_2124, retro_hsap_2198, retro_hsap_2424, retro_hsap_244, retro_hsap_2483, retro_hsap_2486, retro_hsap_250, retro_hsap_282, retro_hsap_2871, retro_hsap_3035, retro_hsap_3097, retro_hsap_3106, retro_hsap_3182, retro_hsap_3211, retro_hsap_3369, retro_hsap_3464, retro_hsap_3584, retro_hsap_3779, retro_hsap_385, retro_hsap_4094, retro_hsap_4290, retro_hsap_435, retro_hsap_4811, retro_hsap_754, retro_hsap_761, retro_hsap_970,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Otolemur garnettii	ENSOGAG00000010098	19 retrocopies	retro_ogar_1051, retro_ogar_1120, retro_ogar_1205, retro_ogar_1557, retro_ogar_1821, retro_ogar_1835, retro_ogar_1837, retro_ogar_1851, retro_ogar_2101, retro_ogar_2164, retro_ogar_2313, retro_ogar_2648, retro_ogar_2817, retro_ogar_2842, retro_ogar_2965, retro_ogar_3109, retro_ogar_3177, retro_ogar_3180, retro_ogar_794,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,

Population studies

Expression level across human populations :

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