RetrogeneDB ID: retro_hsap_3876

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:94324339..94325129(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000232385
• 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_3876
ATGGCAGTTGGCAAGAACAAGTGCTTTATGAAAGGCAGCAAAAAGGGAGCCAAGAAGAAAGTGATTGATCAATTTTCTAA
GAAAGATTGGTATGATGTGAAAGCACTTGCTATGTTCAATATAAGAAATATTGGAAAGACGCCATCACCAGGACCCAAGG
AACCAAAATTGCATCTGATGGTCTCAAGGGTCATGTGTTTGAAGTGAGTCTTGCTGATTTGCAGAATGATGAAGTTGCAT
TTAGAAAATTCAAGCTGATTACTGAAGATGTTCGGGGCAAAAACTGCCTGACTAACTTTCATGGCATGGATCTTACCCAT
GACAAAATGTGTTCCATGGTCAAAAAATGGCAGACAAGATTGAAGCTCACATTGATGTCAAGACTACCGATGGTTACTTG
CTTCATCTGTTCTGTGTTGGTTTTACTAAAAAACACAACAATCAGATACAGAAGACCTCTTATGCTCAGCACCAACAGGT
CCGCCAAATCCAAAAGAAGATGATGGAAATCATGACCTGAGAGGTGCAGACAAATGACTTGAAAGAAGTCGTCAACAAAT
TGATTCCAGACAGCATTGGAAAAGACATAGAAAAGGCTTGCCAATCTATTTATCCTCTCCATGATGTCTTCGTTAGAAAA
GTAAAAATGCTGAAGAAGCCCAAGTTTGAATTGGGAAAGCTCATGGAGCTTCATGGTGACAGCAGTAGTTCTGGAAAAGC
CATTGGGGATGAGACAGGTGCTAAAGTTGAACGAGCTGAGGGATATGAACCACCAGTCCAAGAATCTGTT

Alignment

ORF - retro_hsap_3876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKT-LVTRTQGTKIASDGLKGRVFEV
          MAVGKNK...KG.KKGAKKKV.D.FSKKDWYDVKA.AMFNIRNIGKT...TRTQGTKIASDGLKG.VFEV
Retrocopy MAVGKNKCFMKGSKKGAKKKVIDQFSKKDWYDVKALAMFNIRNIGKT<AITRTQGTKIASDGLKGHVFEV

Parental  SLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM-IEAHVDVKTTDGYLLRLF
          SLADLQNDEVAFRKFKLITEDV.GKNCLTNFHGMDLT.DKMCSMVKKWQT..IEAH.DVKTTDGYLL.LF
Retrocopy SLADLQNDEVAFRKFKLITEDVRGKNCLTNFHGMDLTHDKMCSMVKKWQTR<IEAHIDVKTTDGYLLHLF

Parental  CVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLH
          CVGFTKK.NNQI.KTSYAQHQQVRQI.KKMMEIMT.EVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLH
Retrocopy CVGFTKKHNNQIQKTSYAQHQQVRQIQKKMMEIMT*EVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLH

Parental  DVFVRKVKMLKKPKFELGKLMELHGEGSSSGKATGDETGAKVERADGYEPPVQESV
          DVFVRKVKMLKKPKFELGKLMELHG..SSSGKA.GDETGAKVERA.GYEPPVQESV
Retrocopy DVFVRKVKMLKKPKFELGKLMELHGDSSSSGKAIGDETGAKVERAEGYEPPVQESV

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	0.04 RPM	165.82 RPM
bodymap2_adrenal	0.14 RPM	364.03 RPM
bodymap2_brain	0.00 RPM	75.31 RPM
bodymap2_breast	0.08 RPM	171.42 RPM
bodymap2_colon	0.31 RPM	412.69 RPM
bodymap2_heart	0.00 RPM	106.78 RPM
bodymap2_kidney	0.14 RPM	159.90 RPM
bodymap2_liver	0.02 RPM	109.78 RPM
bodymap2_lung	0.07 RPM	488.03 RPM
bodymap2_lymph_node	0.18 RPM	443.21 RPM
bodymap2_ovary	0.31 RPM	526.47 RPM
bodymap2_prostate	0.17 RPM	540.27 RPM
bodymap2_skeletal_muscle	0.04 RPM	86.34 RPM
bodymap2_testis	0.09 RPM	259.98 RPM
bodymap2_thyroid	0.04 RPM	233.87 RPM
bodymap2_white_blood_cells	0.20 RPM	665.11 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3876 was not detected

EST

No EST(s) were mapped for retro_hsap_3876 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_178501	976 libraries	706 libraries	139 libraries	6 libraries	2 libraries

The graphical summary, for retro_hsap_3876 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_3876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3876 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3076

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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, 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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.07 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.11 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.10 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.11 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.04 RPM

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Indel association:

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