RetrogeneDB ID: retro_hsap_3043

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:62641169..62641568(-)
• Located in intron of: ENSG00000150471

Retrocopy information

• Ensembl ID: ENSG00000226439
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS12
• Ensembl ID: ENSG00000112306
• Aliases: None
• Description: ribosomal protein S12 [Source:HGNC Symbol;Acc:10385]

Sequence

>retro_hsap_3043
ATGGCCGAGGAAGGTATTGCTGCTGGAAGCGTAATGGACGTTAATACTGCTTTACAGGAGGTGCTGAAGACTGCCCTCAT
CCACGATTGCCTAGCACGTGGAATTCATGAAGCTACCAAAGGCTTAGACAAGCACCAAGCCCACCTTTGTGTGCTTGCAT
CCAACTGTGATGAGCCTGTGATGTATGTCAAGTTGGTGGAGGCCCTTTGTGCTGAACACCAAATCAACCTAATTAAGGTT
GATGACAACAAGAAACTAGGGGAAAGGGTAGGCCTCTGTAAAACTGACAGAGAGGGGAAGCCTCATAAAGTGGTTGGTTG
CAGTTGTGCAGTAGTTAAGGACTATGGCAAGGAGTCTCAGGCCAAGGATGTCATCGAAGAGTACTTCAAATGCAAGAAA

Alignment

ORF - retro_hsap_3043 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEEGIAAGGVMDVNTALQEVLKTALIHDGLARGIREAAKALDKRQAHLCVLASNCDEP-MYVKLVEALC
          MAEEGIAAG.VMDVNTALQEVLKTALIHD.LARGI.EA.K.LDK.QAHLCVLASNCDEP.MYVKLVEALC
Retrocopy MAEEGIAAGSVMDVNTALQEVLKTALIHDCLARGIHEATKGLDKHQAHLCVLASNCDEPVMYVKLVEALC

Parental  AEHQINLIKVDDNKKLGEWVGLCKIDREGKPRKVVGCSCVVVKDYGKESQAKDVIEEYFKCKK
          AEHQINLIKVDDNKKLGE.VGLCK.DREGKP.KVVGCSC.VVKDYGKESQAKDVIEEYFKCKK
Retrocopy AEHQINLIKVDDNKKLGERVGLCKTDREGKPHKVVGCSCAVVKDYGKESQAKDVIEEYFKCKK

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	0.06 RPM	474.15 RPM
bodymap2_adrenal	0.00 RPM	588.01 RPM
bodymap2_brain	0.19 RPM	195.61 RPM
bodymap2_breast	0.04 RPM	380.28 RPM
bodymap2_colon	0.06 RPM	575.74 RPM
bodymap2_heart	0.00 RPM	153.01 RPM
bodymap2_kidney	0.02 RPM	295.86 RPM
bodymap2_liver	0.02 RPM	264.93 RPM
bodymap2_lung	0.00 RPM	735.85 RPM
bodymap2_lymph_node	0.00 RPM	1024.27 RPM
bodymap2_ovary	0.10 RPM	823.31 RPM
bodymap2_prostate	0.02 RPM	838.38 RPM
bodymap2_skeletal_muscle	0.00 RPM	323.85 RPM
bodymap2_testis	0.00 RPM	481.66 RPM
bodymap2_thyroid	0.02 RPM	378.38 RPM
bodymap2_white_blood_cells	0.04 RPM	1280.71 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3043 was not detected

EST

No EST(s) were mapped for retro_hsap_3043 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_144643	374 libraries	760 libraries	673 libraries	16 libraries	6 libraries

The graphical summary, for retro_hsap_3043 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_3043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3043 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1995
Gorilla gorilla	retro_ggor_139

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 192 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010479	1 retrocopy	retro_acar_102,
Ailuropoda melanoleuca	ENSAMEG00000008015	2 retrocopies	retro_amel_79, retro_amel_92,
Bos taurus	ENSBTAG00000001360	7 retrocopies	retro_btau_106, retro_btau_1097, retro_btau_1306, retro_btau_1495, retro_btau_1514, retro_btau_1630, retro_btau_1802,
Callithrix jacchus	ENSCJAG00000002865	34 retrocopies	retro_cjac_1038, retro_cjac_1044, retro_cjac_1205, retro_cjac_1291, retro_cjac_1528, retro_cjac_1602, retro_cjac_1778, retro_cjac_1994, retro_cjac_2039, retro_cjac_2058, retro_cjac_2065, retro_cjac_2101, retro_cjac_2112, retro_cjac_2155, retro_cjac_2337, retro_cjac_2406, retro_cjac_2421, retro_cjac_2461, retro_cjac_2681, retro_cjac_2694, retro_cjac_2858, retro_cjac_301, retro_cjac_3310, retro_cjac_4149, retro_cjac_427, retro_cjac_466, retro_cjac_494, retro_cjac_592, retro_cjac_773, retro_cjac_805, retro_cjac_806, retro_cjac_807, retro_cjac_836, retro_cjac_977,
Cavia porcellus	ENSCPOG00000000429	4 retrocopies	retro_cpor_1096, retro_cpor_304, retro_cpor_32, retro_cpor_380,
Equus caballus	ENSECAG00000001599	8 retrocopies	retro_ecab_1012, retro_ecab_1131, retro_ecab_133, retro_ecab_744, retro_ecab_80, retro_ecab_828, retro_ecab_875, retro_ecab_959,
Echinops telfairi	ENSETEG00000006854	14 retrocopies	retro_etel_1129, retro_etel_1512, retro_etel_1580, retro_etel_2016, retro_etel_205, retro_etel_2082, retro_etel_2099, retro_etel_2169, retro_etel_26, retro_etel_280, retro_etel_29, retro_etel_55, retro_etel_578, retro_etel_915,
Felis catus	ENSFCAG00000028402	7 retrocopies	retro_fcat_1084, retro_fcat_1314, retro_fcat_1446, retro_fcat_1880, retro_fcat_537, retro_fcat_664, retro_fcat_796,
Homo sapiens	ENSG00000112306	26 retrocopies	retro_hsap_1241, retro_hsap_1522, retro_hsap_1738, retro_hsap_1771, retro_hsap_1797, retro_hsap_1962, retro_hsap_1992, retro_hsap_2249, retro_hsap_2264, retro_hsap_2667, retro_hsap_2722, retro_hsap_3043 , retro_hsap_3079, retro_hsap_3249, retro_hsap_3347, retro_hsap_3428, retro_hsap_3467, retro_hsap_3640, retro_hsap_3680, retro_hsap_3994, retro_hsap_4130, retro_hsap_599, retro_hsap_661, retro_hsap_702, retro_hsap_824, retro_hsap_895,
Gorilla gorilla	ENSGGOG00000012234	22 retrocopies	retro_ggor_1164, retro_ggor_1287, retro_ggor_1322, retro_ggor_139, retro_ggor_1426, retro_ggor_1441, retro_ggor_1686, retro_ggor_1861, retro_ggor_1894, retro_ggor_2115, retro_ggor_2241, retro_ggor_2261, retro_ggor_2339, retro_ggor_2456, retro_ggor_2489, retro_ggor_2680, retro_ggor_3076, retro_ggor_530, retro_ggor_595, retro_ggor_673, retro_ggor_724, retro_ggor_971,
Gadus morhua	ENSGMOG00000019455	1 retrocopy	retro_gmor_11,
Microcebus murinus	ENSMICG00000005252	5 retrocopies	retro_mmur_1260, retro_mmur_1527, retro_mmur_391, retro_mmur_491, retro_mmur_98,
Myotis lucifugus	ENSMLUG00000001137	5 retrocopies	retro_mluc_1479, retro_mluc_1552, retro_mluc_1987, retro_mluc_1988, retro_mluc_582,
Macaca mulatta	ENSMMUG00000013237	1 retrocopy	retro_mmul_12,
Monodelphis domestica	ENSMODG00000017520	1 retrocopy	retro_mdom_779,
Mustela putorius furo	ENSMPUG00000014771	1 retrocopy	retro_mputfur_6,
Mus musculus	ENSMUSG00000061983	1 retrocopy	retro_mmus_36,
Pelodiscus sinensis	ENSPSIG00000003457	1 retrocopy	retro_psin_52,
Rattus norvegicus	ENSRNOG00000016411	5 retrocopies	retro_rnor_177, retro_rnor_186, retro_rnor_241, retro_rnor_295, retro_rnor_300,
Sorex araneus	ENSSARG00000003170	2 retrocopies	retro_sara_356, retro_sara_8,
Sarcophilus harrisii	ENSSHAG00000008905	6 retrocopies	retro_shar_187, retro_shar_226, retro_shar_475, retro_shar_492, retro_shar_621, retro_shar_671,
Tarsius syrichta	ENSTSYG00000010097	24 retrocopies	retro_tsyr_1010, retro_tsyr_102, retro_tsyr_1123, retro_tsyr_1188, retro_tsyr_129, retro_tsyr_1313, retro_tsyr_1345, retro_tsyr_1398, retro_tsyr_1486, retro_tsyr_1668, retro_tsyr_1955, retro_tsyr_1993, retro_tsyr_205, retro_tsyr_249, retro_tsyr_303, retro_tsyr_419, retro_tsyr_453, retro_tsyr_556, retro_tsyr_645, retro_tsyr_733, retro_tsyr_764, retro_tsyr_801, retro_tsyr_970, retro_tsyr_99,
Tursiops truncatus	ENSTTRG00000000609	11 retrocopies	retro_ttru_1290, retro_ttru_206, retro_ttru_233, retro_ttru_304, retro_ttru_559, retro_ttru_64, retro_ttru_667, retro_ttru_727, retro_ttru_787, retro_ttru_955, retro_ttru_990,
Vicugna pacos	ENSVPAG00000011504	3 retrocopies	retro_vpac_133, retro_vpac_267, retro_vpac_339,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.15 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.08 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.05 RPM
YRI_NA19214	0.07 RPM
YRI_NA19223	0.00 RPM

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Indel association:

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