RetrogeneDB ID: retro_hsap_1835

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:41321896..41322094(-)
• Located in intron of: ENSG00000267002

Retrocopy information

• Ensembl ID: ENSG00000267340
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPLP1
• Ensembl ID: ENSG00000137818
• Aliases: RPLP1, LP1, P1, RPP1
• Description: ribosomal protein, large, P1 [Source:HGNC Symbol;Acc:10372]

Sequence

>retro_hsap_1835
ATGGCCTCCGTCTCCCAGCTTGCCTGCATCTACTCTGCCCTCATTCTGCAGGACTATGAGGTGACCTTTACGGAGGATAA
GATCAATGCCCTTATTAAAGCAGCCAGTGTAAATATTGAAACTTTTTGGCCTGGCTTGTTTGCAAAGGTCCTGGCCAACG
TCAACATTGGGAGCCACATCTGCAGTGTAGAGGGGGGG

Alignment

ORF - retro_hsap_1835 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 57.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASVSELACIYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKALANVNIGSLICNVGAG
          MASVS.LACIYSALIL.D.EVT.TEDKINALIKAA.VN.E.FWPGLFAK.LANVNIGS.IC.V..G
Retrocopy MASVSQLACIYSALILQDYEVTFTEDKINALIKAASVNIETFWPGLFAKVLANVNIGSHICSVEGG

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	0.00 RPM	427.30 RPM
bodymap2_adrenal	0.20 RPM	725.01 RPM
bodymap2_brain	0.19 RPM	87.55 RPM
bodymap2_breast	0.02 RPM	301.89 RPM
bodymap2_colon	0.04 RPM	579.73 RPM
bodymap2_heart	0.18 RPM	216.12 RPM
bodymap2_kidney	0.06 RPM	277.51 RPM
bodymap2_liver	0.04 RPM	291.89 RPM
bodymap2_lung	0.14 RPM	786.06 RPM
bodymap2_lymph_node	0.42 RPM	987.56 RPM
bodymap2_ovary	0.10 RPM	567.51 RPM
bodymap2_prostate	0.02 RPM	839.59 RPM
bodymap2_skeletal_muscle	0.00 RPM	1616.35 RPM
bodymap2_testis	0.25 RPM	367.99 RPM
bodymap2_thyroid	0.17 RPM	263.03 RPM
bodymap2_white_blood_cells	0.00 RPM	956.87 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_1835 in 34 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	17:41322066..41322228
ENCFF002CFW	POLR2A	17:41322245..41322675
ENCFF002CFX	POLR2A	17:41322882..41323137
ENCFF002CHO	POLR2A	17:41322764..41323588
ENCFF002CJE	POLR2A	17:41322845..41323430
ENCFF002CJZ	POLR2A	17:41322844..41323462
ENCFF002CJZ	POLR2A	17:41322346..41322686
ENCFF002CKX	POLR2A	17:41322838..41323193
ENCFF002CKX	POLR2A	17:41322023..41322214
ENCFF002CLM	POLR2A	17:41322993..41323533
ENCFF002CMI	POLR2A	17:41322803..41323626
ENCFF002CMI	POLR2A	17:41322331..41322757
ENCFF002CPG	POLR2A	17:41322318..41322808
ENCFF002CPH	POLR2A	17:41323051..41323441
ENCFF002CPH	POLR2A	17:41322390..41322780
ENCFF002CQA	POLR2A	17:41323008..41323578
ENCFF002CQA	POLR2A	17:41322242..41322812
ENCFF002CQA	POLR2A	17:41322879..41323026
ENCFF002CQC	POLR2A	17:41322733..41323213
ENCFF002CQG	POLR2A	17:41322713..41323237
ENCFF002CQO	POLR2A	17:41322699..41323229
ENCFF002CRK	POLR2A	17:41323027..41323551
ENCFF002CSY	POLR2A	17:41322313..41323544
ENCFF002CVJ	POLR2A	17:41323091..41323479
ENCFF002CVJ	POLR2A	17:41322166..41322776
ENCFF002CXM	POLR2A	17:41322318..41322808
ENCFF002CXM	POLR2A	17:41323006..41323496
ENCFF002CXN	POLR2A	17:41322360..41322856
ENCFF002CXN	POLR2A	17:41323047..41323543
ENCFF002CXO	POLR2A	17:41322336..41322760
ENCFF002CXP	POLR2A	17:41323011..41323491
ENCFF002CXR	POLR2A	17:41322855..41323182
ENCFF002CXR	POLR2A	17:41322399..41322672
ENCFF002CZC	POLR2A	17:41322782..41323494
ENCFF002CZC	POLR2A	17:41322279..41322761
ENCFF002CZD	POLR2A	17:41322826..41323460
ENCFF002CZD	POLR2A	17:41322340..41322672
ENCFF002CZQ	POLR2A	17:41322818..41323268
ENCFF002CZQ	POLR2A	17:41323028..41323478
ENCFF002CZQ	POLR2A	17:41322276..41322726
ENCFF002CZW	POLR2A	17:41322284..41323495
ENCFF002CZY	POLR2A	17:41322363..41322681
ENCFF002DAK	POLR2A	17:41322995..41323495
ENCFF002DAS	POLR2A	17:41323010..41323486
ENCFF002DAV	POLR2A	17:41322991..41323535
ENCFF002DAY	POLR2A	17:41322638..41323274
ENCFF002DBB	POLR2A	17:41322866..41323066
ENCFF002DBE	POLR2A	17:41322305..41322801
ENCFF002DBT	POLR2A	17:41323076..41323446

EST

No EST(s) were mapped for retro_hsap_1835 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_58953	182 libraries	263 libraries	1196 libraries	167 libraries	21 libraries
TSS #2	TSS_58954	238 libraries	334 libraries	1147 libraries	94 libraries	16 libraries
TSS #3	TSS_58955	345 libraries	458 libraries	949 libraries	71 libraries	6 libraries

The graphical summary, for retro_hsap_1835 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_1835 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1835 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 174 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018320	4 retrocopies	retro_btau_1131, retro_btau_1717, retro_btau_186, retro_btau_615,
Callithrix jacchus	ENSCJAG00000032919	19 retrocopies	retro_cjac_1125, retro_cjac_1150, retro_cjac_1222, retro_cjac_1375, retro_cjac_1413, retro_cjac_1666, retro_cjac_1809, retro_cjac_183, retro_cjac_2090, retro_cjac_2626, retro_cjac_267, retro_cjac_2765, retro_cjac_306, retro_cjac_3131, retro_cjac_458, retro_cjac_469, retro_cjac_694, retro_cjac_750, retro_cjac_984,
Equus caballus	ENSECAG00000008542	4 retrocopies	retro_ecab_380, retro_ecab_677, retro_ecab_820, retro_ecab_958,
Homo sapiens	ENSG00000137818	18 retrocopies	retro_hsap_1325, retro_hsap_1366, retro_hsap_1719, retro_hsap_1835 , retro_hsap_2014, retro_hsap_2079, retro_hsap_2348, retro_hsap_2897, retro_hsap_2936, retro_hsap_3169, retro_hsap_3382, retro_hsap_3392, retro_hsap_3523, retro_hsap_3768, retro_hsap_3939, retro_hsap_472, retro_hsap_533, retro_hsap_679,
Gorilla gorilla	ENSGGOG00000003980	13 retrocopies	retro_ggor_1033, retro_ggor_118, retro_ggor_1276, retro_ggor_1458, retro_ggor_1628, retro_ggor_2036, retro_ggor_2163, retro_ggor_2269, retro_ggor_2381, retro_ggor_2534, retro_ggor_585, retro_ggor_73, retro_ggor_94,
Latimeria chalumnae	ENSLACG00000012630	1 retrocopy	retro_lcha_7,
Macropus eugenii	ENSMEUG00000015277	6 retrocopies	retro_meug_1096, retro_meug_1283, retro_meug_1312, retro_meug_1401, retro_meug_1515, retro_meug_793,
Myotis lucifugus	ENSMLUG00000010542	33 retrocopies	retro_mluc_10, retro_mluc_1064, retro_mluc_1122, retro_mluc_1234, retro_mluc_136, retro_mluc_1374, retro_mluc_1412, retro_mluc_1424, retro_mluc_1654, retro_mluc_1670, retro_mluc_1751, retro_mluc_1810, retro_mluc_1832, retro_mluc_1850, retro_mluc_1944, retro_mluc_197, retro_mluc_2025, retro_mluc_2255, retro_mluc_2265, retro_mluc_2294, retro_mluc_2489, retro_mluc_2578, retro_mluc_433, retro_mluc_472, retro_mluc_570, retro_mluc_577, retro_mluc_61, retro_mluc_732, retro_mluc_791, retro_mluc_858, retro_mluc_916, retro_mluc_945, retro_mluc_95,
Monodelphis domestica	ENSMODG00000009209	1 retrocopy	retro_mdom_1022,
Mustela putorius furo	ENSMPUG00000000204	13 retrocopies	retro_mputfur_1018, retro_mputfur_113, retro_mputfur_122, retro_mputfur_1265, retro_mputfur_129, retro_mputfur_1334, retro_mputfur_1450, retro_mputfur_1598, retro_mputfur_1613, retro_mputfur_304, retro_mputfur_628, retro_mputfur_635, retro_mputfur_709,
Mus musculus	ENSMUSG00000007892	6 retrocopies	retro_mmus_180, retro_mmus_206, retro_mmus_2060, retro_mmus_2180, retro_mmus_247, retro_mmus_2525,
Oryctolagus cuniculus	ENSOCUG00000015087	8 retrocopies	retro_ocun_1009, retro_ocun_1464, retro_ocun_1655, retro_ocun_1735, retro_ocun_48, retro_ocun_551, retro_ocun_647, retro_ocun_884,
Otolemur garnettii	ENSOGAG00000029641	19 retrocopies	retro_ogar_1078, retro_ogar_1259, retro_ogar_1363, retro_ogar_1430, retro_ogar_1670, retro_ogar_2215, retro_ogar_2413, retro_ogar_2603, retro_ogar_2683, retro_ogar_2942, retro_ogar_3053, retro_ogar_3222, retro_ogar_3393, retro_ogar_363, retro_ogar_474, retro_ogar_500, retro_ogar_574, retro_ogar_607, retro_ogar_961,
Procavia capensis	ENSPCAG00000014595	7 retrocopies	retro_pcap_107, retro_pcap_118, retro_pcap_124, retro_pcap_315, retro_pcap_32, retro_pcap_36, retro_pcap_83,
Pongo abelii	ENSPPYG00000006601	5 retrocopies	retro_pabe_1506, retro_pabe_160, retro_pabe_182, retro_pabe_261, retro_pabe_3080,
Rattus norvegicus	ENSRNOG00000011955	6 retrocopies	retro_rnor_1042, retro_rnor_1402, retro_rnor_1827, retro_rnor_2175, retro_rnor_2678, retro_rnor_493,
Rattus norvegicus	ENSRNOG00000013874	3 retrocopies	retro_rnor_2432, retro_rnor_2700, retro_rnor_2934,
Ictidomys tridecemlineatus	ENSSTOG00000027893	8 retrocopies	retro_itri_1589, retro_itri_1698, retro_itri_1842, retro_itri_1856, retro_itri_226, retro_itri_409, retro_itri_796, retro_itri_976,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.33 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.41 RPM
CEU_NA12760	0.31 RPM
CEU_NA12827	0.42 RPM
CEU_NA12872	0.27 RPM
CEU_NA12873	0.29 RPM
FIN_HG00183	0.22 RPM
FIN_HG00277	0.30 RPM
FIN_HG00315	0.19 RPM
FIN_HG00321	0.27 RPM
FIN_HG00328	0.17 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.11 RPM
FIN_HG00375	0.24 RPM
FIN_HG00377	0.08 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.17 RPM
GBR_HG00111	0.15 RPM
GBR_HG00114	0.32 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.14 RPM
GBR_HG00133	0.19 RPM
GBR_HG00134	0.24 RPM
GBR_HG00137	0.19 RPM
GBR_HG00142	0.39 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.20 RPM
TSI_NA20513	0.39 RPM
TSI_NA20518	0.22 RPM
TSI_NA20532	0.34 RPM
TSI_NA20538	0.28 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.12 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.16 RPM
TSI_NA20798	0.28 RPM
YRI_NA18870	0.24 RPM
YRI_NA18907	0.28 RPM
YRI_NA18916	0.36 RPM
YRI_NA19093	0.16 RPM
YRI_NA19099	0.24 RPM
YRI_NA19114	0.10 RPM
YRI_NA19118	0.12 RPM
YRI_NA19213	0.19 RPM
YRI_NA19214	0.22 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).