RetrogeneDB ID: retro_hsap_1812

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:19349285..19350165(-)
• Located in intron of: ENSG00000235979

Retrocopy information

• Ensembl ID: ENSG00000189343
• 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_1812
ATGGCGGATGACGCCGGTGCAGCGGGGGGGCCCGGAGGCCCTGGTGGCCCTGAGATGGGGAACCGCGGTGGCTTCCGCGG
AGGTTTCGGCAGTGGCATCCGGGGCCAGGGTCGCGGCCGTGGACGGGGCCGGGGCCAAGGCCGCGGAGCTCGCGGAGGCA
AGGCCGAGGATAAGGAGTGGATGCCCGTCACCAAGTTGGGCCGCTTGGTCAAGGACATGAAGATCAAGTCCCTGGAGGAG
ATCTATCTCTTCTCCCTGCCCAATTAAGGAATCAGAGATCATTGATTTCTTCCTGGGGGCCTCTCTCAAGGATGAGGTTT
TGAAGATTATGCCAGTGCAGAAGCAGACCCGTGCCGGCCAGCGCACCAGGTTCAAGGCATTTGTTGCTATCGGGGACTAC
AACGGCCACGTCGGTCTGGGTGTTAAGTGCTCCAAGGAGGTGGCCACCGCCATCCGTGGGGCCATCATCCTGGCCAAGCT
CTCCATCGTCCCCGTGCGCAGAGGCTACTGGGGGAACAAGATCGGCAAGCCCCACACTGTCCCTTGCAAGGTGACAGGCT
GCTGCGGCTCTGTGCTGGTACGCCTCATCCCTGCACCCAGGGGCACTGGCATCGTCTCCGCACCTGTGCCTAAGAAGCTG
CTCATGATGGCTGGTATCGATGACTGCTACACCTCAGCCCGGGGCTGCACTGCCACCCTGGGCAACTTCACCAAGGCCAC
CTTTGATGCCATTTCTAAGACCTACAGCTACCTAACCCCCGACCTCTGGAAGGAGACTGTATTTACCAAGTCTCCCTATC
AGGAATTCACTGACCACCTCGTCAAGACCCACACCAGAGTCTCCGTGCAGCGGACTCAGGCTCCAGCTGTGGCTACAACA

Alignment

ORF - retro_hsap_1812 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEWMPVTKLGRLV
          MADDAGAAGGPGGPGGP.MGNRGGFRGGFGSGIRG.GRGRGRGRG.GRGARGGKAEDKEWMPVTKLGRLV
Retrocopy MADDAGAAGGPGGPGGPEMGNRGGFRGGFGSGIRGQGRGRGRGRGQGRGARGGKAEDKEWMPVTKLGRLV

Parental  KDMKIKSLEEIYLFSL-PIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGL
          KDMKIKSLEEIYLFSL.PIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGL
Retrocopy KDMKIKSLEEIYLFSL>PIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGL

Parental  GVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPV
          GVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTG.CGSVLVRLIPAPRGTGIVSAPV
Retrocopy GVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGCCGSVLVRLIPAPRGTGIVSAPV

Parental  PKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTR
          PKKLLMMAGIDDCYTSARGCTATLGNF.KATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTR
Retrocopy PKKLLMMAGIDDCYTSARGCTATLGNFTKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTR

Parental  VSVQRTQAPAVATT
          VSVQRTQAPAVATT
Retrocopy VSVQRTQAPAVATT

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	18.33 RPM	496.47 RPM
bodymap2_adrenal	45.52 RPM	505.10 RPM
bodymap2_brain	0.96 RPM	53.79 RPM
bodymap2_breast	10.97 RPM	261.89 RPM
bodymap2_colon	16.73 RPM	444.16 RPM
bodymap2_heart	8.22 RPM	116.21 RPM
bodymap2_kidney	2.28 RPM	179.65 RPM
bodymap2_liver	7.67 RPM	249.89 RPM
bodymap2_lung	8.86 RPM	464.79 RPM
bodymap2_lymph_node	8.57 RPM	651.42 RPM
bodymap2_ovary	41.87 RPM	445.62 RPM
bodymap2_prostate	18.24 RPM	603.00 RPM
bodymap2_skeletal_muscle	21.63 RPM	731.68 RPM
bodymap2_testis	4.69 RPM	238.89 RPM
bodymap2_thyroid	0.77 RPM	257.52 RPM
bodymap2_white_blood_cells	28.27 RPM	782.33 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1812 was not detected

EST

No EST(s) were mapped for retro_hsap_1812 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_56166	1 library	0 libraries	0 libraries	1 library	1827 libraries

The graphical summary, for retro_hsap_1812 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_1812 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1812 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 :

Library	Retrogene expression
CEU_NA11831	13.78 RPM
CEU_NA11843	29.00 RPM
CEU_NA11930	15.48 RPM
CEU_NA12004	13.26 RPM
CEU_NA12400	13.05 RPM
CEU_NA12751	10.78 RPM
CEU_NA12760	22.05 RPM
CEU_NA12827	13.49 RPM
CEU_NA12872	10.04 RPM
CEU_NA12873	18.19 RPM
FIN_HG00183	17.76 RPM
FIN_HG00277	18.45 RPM
FIN_HG00315	9.27 RPM
FIN_HG00321	15.17 RPM
FIN_HG00328	9.35 RPM
FIN_HG00338	18.22 RPM
FIN_HG00349	14.37 RPM
FIN_HG00375	19.39 RPM
FIN_HG00377	14.04 RPM
FIN_HG00378	16.34 RPM
GBR_HG00099	10.03 RPM
GBR_HG00111	9.39 RPM
GBR_HG00114	13.67 RPM
GBR_HG00119	10.35 RPM
GBR_HG00131	11.41 RPM
GBR_HG00133	9.19 RPM
GBR_HG00134	12.43 RPM
GBR_HG00137	13.47 RPM
GBR_HG00142	9.84 RPM
GBR_HG00143	8.17 RPM
TSI_NA20512	17.49 RPM
TSI_NA20513	14.82 RPM
TSI_NA20518	22.04 RPM
TSI_NA20532	5.20 RPM
TSI_NA20538	13.91 RPM
TSI_NA20756	12.16 RPM
TSI_NA20765	10.51 RPM
TSI_NA20771	17.64 RPM
TSI_NA20786	15.09 RPM
TSI_NA20798	14.10 RPM
YRI_NA18870	14.52 RPM
YRI_NA18907	12.86 RPM
YRI_NA18916	15.43 RPM
YRI_NA19093	16.97 RPM
YRI_NA19099	13.95 RPM
YRI_NA19114	18.95 RPM
YRI_NA19118	16.88 RPM
YRI_NA19213	8.63 RPM
YRI_NA19214	12.79 RPM
YRI_NA19223	12.34 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).