RetrogeneDB ID: retro_hsap_3454

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:34711952..34712447(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000217130
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS10
• Ensembl ID: ENSG00000124614
• Aliases: RPS10, DBA9, S10
• Description: ribosomal protein S10 [Source:HGNC Symbol;Acc:10383]

Sequence

>retro_hsap_3454
ATGTTGATGCCTAAGAAGAACCGGATTGCCATTTATGAACTCCTTTTTAAGAAGGGAGTCATGGTGGCCAAGAAGGATGT
CCACATGCCTAAGCACCCGGAGCTGGCAGACAAGAATGTGCCCAACCTTCATGTCATGAAAGCCATGCAGTCTCTCTAGT
CCCGAGGCTACGTGAAGGAACAGTTTGCCTGGAGACATTTCTACTGGTACCTTACCAATGAGGGTATCCAGTATCTCCAT
GATTACCTTCATCTGCCCCCGGAGATTGTGCCTGCCACCCTACGCCGTAGGCATCCAGAGACTGGCAGGCCTCGGCCTAA
AGGTCTGGAGGGTGAGCAACCTGCGAGACTCACAAGATGGGAAGCTGACAGAGATACCTACAGACAGAGTGCTGTGCCAC
CTGGTGCCGACAAGAAAGCCGAGTCTGGGGCTGGGTCAGCAACTGAATTCCAGTTTAGAGGCGGATTTGGTTGTGGACAT
AGTCAGCTACCTCAG

Alignment

ORF - retro_hsap_3454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWY
          MLMPKKNRIAIYELLFK.GVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSL.SRGYVKEQFAWRHFYWY
Retrocopy MLMPKKNRIAIYELLFKKGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSL*SRGYVKEQFAWRHFYWY

Parental  LTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRGEADRDTYRRSAVPPGADKKA
          LTNEGIQYL.DYLHLPPEIVPATLRR..PETGRPRPKGLEGE.PARLTR.EADRDTYR.SAVPPGADKKA
Retrocopy LTNEGIQYLHDYLHLPPEIVPATLRRRHPETGRPRPKGLEGEQPARLTRWEADRDTYRQSAVPPGADKKA

Parental  EAGAGSATEFQFRGGFGRGRGQPPQ
          E.GAGSATEFQFRGGFG.G..Q.PQ
Retrocopy ESGAGSATEFQFRGGFGCGHSQLPQ

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	0.95 RPM	30.51 RPM
bodymap2_adrenal	0.94 RPM	65.30 RPM
bodymap2_brain	0.23 RPM	3.61 RPM
bodymap2_breast	0.97 RPM	33.87 RPM
bodymap2_colon	1.02 RPM	20.48 RPM
bodymap2_heart	0.04 RPM	1.90 RPM
bodymap2_kidney	0.39 RPM	6.35 RPM
bodymap2_liver	0.32 RPM	2.53 RPM
bodymap2_lung	0.51 RPM	7.21 RPM
bodymap2_lymph_node	0.95 RPM	9.17 RPM
bodymap2_ovary	1.75 RPM	57.73 RPM
bodymap2_prostate	0.85 RPM	8.95 RPM
bodymap2_skeletal_muscle	0.65 RPM	3.66 RPM
bodymap2_testis	0.75 RPM	14.37 RPM
bodymap2_thyroid	1.13 RPM	25.57 RPM
bodymap2_white_blood_cells	1.34 RPM	9.71 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3454 was not detected

EST

No EST(s) were mapped for retro_hsap_3454 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_165003	109 libraries	41 libraries	431 libraries	481 libraries	767 libraries

The graphical summary, for retro_hsap_3454 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_3454 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3454 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2342

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 139 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015250	4 retrocopies	retro_cjac_215, retro_cjac_296, retro_cjac_325, retro_cjac_63,
Dasypus novemcinctus	ENSDNOG00000011670	2 retrocopies	retro_dnov_2303, retro_dnov_2558,
Dipodomys ordii	ENSDORG00000012060	6 retrocopies	retro_dord_225, retro_dord_494, retro_dord_641, retro_dord_73, retro_dord_74, retro_dord_767,
Equus caballus	ENSECAG00000006430	1 retrocopy	retro_ecab_198,
Homo sapiens	ENSG00000124614	24 retrocopies	retro_hsap_1509, retro_hsap_1628, retro_hsap_1630, retro_hsap_1657, retro_hsap_1923, retro_hsap_2003, retro_hsap_2113, retro_hsap_229, retro_hsap_2415, retro_hsap_2573, retro_hsap_2574, retro_hsap_2830, retro_hsap_289, retro_hsap_3007, retro_hsap_3170, retro_hsap_3243, retro_hsap_3436, retro_hsap_3454 , retro_hsap_3720, retro_hsap_4114, retro_hsap_4190, retro_hsap_460, retro_hsap_869, retro_hsap_992,
Latimeria chalumnae	ENSLACG00000017219	1 retrocopy	retro_lcha_26,
Loxodonta africana	ENSLAFG00000008539	1 retrocopy	retro_lafr_756,
Macaca mulatta	ENSMMUG00000000267	2 retrocopies	retro_mmul_332, retro_mmul_555,
Monodelphis domestica	ENSMODG00000013929	2 retrocopies	retro_mdom_1889, retro_mdom_437,
Mus musculus	ENSMUSG00000052146	9 retrocopies	retro_mmus_1376, retro_mmus_1500, retro_mmus_1831, retro_mmus_2431, retro_mmus_2551, retro_mmus_2708, retro_mmus_3651, retro_mmus_5, retro_mmus_858,
Nomascus leucogenys	ENSNLEG00000008336	24 retrocopies	retro_nleu_1064, retro_nleu_1206, retro_nleu_1217, retro_nleu_1366, retro_nleu_1463, retro_nleu_1496, retro_nleu_165, retro_nleu_1694, retro_nleu_1748, retro_nleu_1969, retro_nleu_2120, retro_nleu_2452, retro_nleu_2678, retro_nleu_2791, retro_nleu_2833, retro_nleu_2834, retro_nleu_2950, retro_nleu_2955, retro_nleu_3021, retro_nleu_3047, retro_nleu_3052, retro_nleu_579, retro_nleu_850, retro_nleu_882,
Oryctolagus cuniculus	ENSOCUG00000011373	2 retrocopies	retro_ocun_250, retro_ocun_874,
Ochotona princeps	ENSOPRG00000002693	2 retrocopies	retro_opri_297, retro_opri_800,
Procavia capensis	ENSPCAG00000012795	1 retrocopy	retro_pcap_309,
Pongo abelii	ENSPPYG00000016516	2 retrocopies	retro_pabe_2319, retro_pabe_97,
Pan troglodytes	ENSPTRG00000018063	26 retrocopies	retro_ptro_1021, retro_ptro_1090, retro_ptro_1092, retro_ptro_1126, retro_ptro_1160, retro_ptro_1287, retro_ptro_1335, retro_ptro_1391, retro_ptro_1497, retro_ptro_1502, retro_ptro_1503, retro_ptro_1788, retro_ptro_1918, retro_ptro_199, retro_ptro_2192, retro_ptro_2330, retro_ptro_2342, retro_ptro_238, retro_ptro_2519, retro_ptro_2793, retro_ptro_2797, retro_ptro_2919, retro_ptro_3051, retro_ptro_3078, retro_ptro_347, retro_ptro_603,
Rattus norvegicus	ENSRNOG00000000490	4 retrocopies	retro_rnor_169, retro_rnor_224, retro_rnor_359, retro_rnor_74,
Sarcophilus harrisii	ENSSHAG00000000731	3 retrocopies	retro_shar_243, retro_shar_334, retro_shar_724,
Ictidomys tridecemlineatus	ENSSTOG00000013486	5 retrocopies	retro_itri_1448, retro_itri_1515, retro_itri_230, retro_itri_787, retro_itri_963,
Tupaia belangeri	ENSTBEG00000001492	16 retrocopies	retro_tbel_1302, retro_tbel_175, retro_tbel_1775, retro_tbel_2039, retro_tbel_2061, retro_tbel_2062, retro_tbel_2766, retro_tbel_2814, retro_tbel_314, retro_tbel_3359, retro_tbel_483, retro_tbel_522, retro_tbel_667, retro_tbel_980, retro_tbel_981, retro_tbel_986,
Tursiops truncatus	ENSTTRG00000015064	2 retrocopies	retro_ttru_1089, retro_ttru_1211,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.62 RPM
CEU_NA11843	0.43 RPM
CEU_NA11930	0.52 RPM
CEU_NA12004	0.15 RPM
CEU_NA12400	1.12 RPM
CEU_NA12751	1.17 RPM
CEU_NA12760	1.35 RPM
CEU_NA12827	0.80 RPM
CEU_NA12872	0.82 RPM
CEU_NA12873	0.73 RPM
FIN_HG00183	1.18 RPM
FIN_HG00277	0.55 RPM
FIN_HG00315	1.41 RPM
FIN_HG00321	0.54 RPM
FIN_HG00328	1.02 RPM
FIN_HG00338	1.36 RPM
FIN_HG00349	0.54 RPM
FIN_HG00375	0.34 RPM
FIN_HG00377	1.08 RPM
FIN_HG00378	0.79 RPM
GBR_HG00099	0.78 RPM
GBR_HG00111	1.38 RPM
GBR_HG00114	0.53 RPM
GBR_HG00119	1.15 RPM
GBR_HG00131	0.92 RPM
GBR_HG00133	0.60 RPM
GBR_HG00134	0.83 RPM
GBR_HG00137	1.07 RPM
GBR_HG00142	0.25 RPM
GBR_HG00143	0.45 RPM
TSI_NA20512	0.51 RPM
TSI_NA20513	0.34 RPM
TSI_NA20518	0.39 RPM
TSI_NA20532	0.75 RPM
TSI_NA20538	0.60 RPM
TSI_NA20756	1.31 RPM
TSI_NA20765	0.83 RPM
TSI_NA20771	1.87 RPM
TSI_NA20786	1.02 RPM
TSI_NA20798	0.59 RPM
YRI_NA18870	0.74 RPM
YRI_NA18907	0.31 RPM
YRI_NA18916	1.26 RPM
YRI_NA19093	0.29 RPM
YRI_NA19099	1.04 RPM
YRI_NA19114	1.10 RPM
YRI_NA19118	0.39 RPM
YRI_NA19213	1.08 RPM
YRI_NA19214	0.37 RPM
YRI_NA19223	0.36 RPM

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Indel association:

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