RetrogeneDB ID:

retro_hsap_2014

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:19:54278852..54279064(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000238150
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPLP1
Ensembl ID:ENSG00000137818
Aliases:RPLP1, LP1, P1, RPP1
Description:ribosomal protein, large, P1 [Source:HGNC Symbol;Acc:10372]


Retrocopy-Parental alignment summary:






>retro_hsap_2014
ATGGCCTCTGTCTCCGAGCTCGCCTGCATCTACTAGGCGCTCATTCTGCACGACGATGAGGTGACCGTCACGGAGGATAA
GATCAATGCTCTCATTAAAGCAGCTGGTGTAAATATTGAACCTTTTTGACCTGGCTTGTTTGCAAAGGCCTGGTCAATGT
CAACATCGGGAGCCTCATCTGCAGTGTAGAGGCTGGTGGAGCTGCTCCAGCT

ORF - retro_hsap_2014 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.89 %
Parental protein coverage: 62.28 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMASVSELACIYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPGLFAKA-LANVNIGSLICNVGAGGPA
MASVSELACIY.ALILHDDEVTVTEDKINALIKAAGVN.EPF.PGLFAKA.L.NVNIGSLIC.V.AGG.A
RetrocopyMASVSELACIY*ALILHDDEVTVTEDKINALIKAAGVNIEPF*PGLFAKA<LVNVNIGSLICSVEAGGAA
ParentalPA
PA
RetrocopyPA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .08 RPM 427 .30 RPM
bodymap2_adrenal 0 .06 RPM 725 .01 RPM
bodymap2_brain 0 .00 RPM 87 .55 RPM
bodymap2_breast 0 .00 RPM 301 .89 RPM
bodymap2_colon 0 .06 RPM 579 .73 RPM
bodymap2_heart 0 .00 RPM 216 .12 RPM
bodymap2_kidney 0 .00 RPM 277 .51 RPM
bodymap2_liver 0 .00 RPM 291 .89 RPM
bodymap2_lung 0 .00 RPM 786 .06 RPM
bodymap2_lymph_node 0 .00 RPM 987 .56 RPM
bodymap2_ovary 0 .13 RPM 567 .51 RPM
bodymap2_prostate 0 .03 RPM 839 .59 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1616 .35 RPM
bodymap2_testis 0 .04 RPM 367 .99 RPM
bodymap2_thyroid 0 .13 RPM 263 .03 RPM
bodymap2_white_blood_cells 0 .00 RPM 956 .87 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_2014 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 19:54278563..54278993

EST - click to see more details

No EST(s) were mapped for retro_hsap_2014 retrocopy.

TSS - click to see more details



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_77757127 libraries225 libraries927 libraries357 libraries193 libraries

The graphical summary, for retro_hsap_2014 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)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_2014 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2014 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1458
Parental genes homology:
Parental genes homology involve 18 parental genes, and 174 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000183204 retrocopies
retro_btau_1131, retro_btau_1717, retro_btau_186, retro_btau_615,
Callithrix jacchus ENSCJAG0000003291919 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 ENSECAG000000085424 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 ENSGGOG0000000398013 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 ENSLACG000000126301 retrocopy
retro_lcha_7,
Macropus eugenii ENSMEUG000000152776 retrocopies
retro_meug_1096, retro_meug_1283, retro_meug_1312, retro_meug_1401, retro_meug_1515, retro_meug_793,
Myotis lucifugus ENSMLUG0000001054233 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 ENSMODG000000092091 retrocopy
retro_mdom_1022,
Mustela putorius furoENSMPUG0000000020413 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 ENSMUSG000000078926 retrocopies
retro_mmus_180, retro_mmus_206, retro_mmus_2060, retro_mmus_2180, retro_mmus_247, retro_mmus_2525,
Oryctolagus cuniculus ENSOCUG000000150878 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 ENSOGAG0000002964119 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 ENSPCAG000000145957 retrocopies
retro_pcap_107, retro_pcap_118, retro_pcap_124, retro_pcap_315, retro_pcap_32, retro_pcap_36, retro_pcap_83,
Pongo abelii ENSPPYG000000066015 retrocopies
retro_pabe_1506, retro_pabe_160, retro_pabe_182, retro_pabe_261, retro_pabe_3080,
Rattus norvegicus ENSRNOG000000119556 retrocopies
retro_rnor_1042, retro_rnor_1402, retro_rnor_1827, retro_rnor_2175, retro_rnor_2678, retro_rnor_493,
Rattus norvegicus ENSRNOG000000138743 retrocopies
retro_rnor_2432, retro_rnor_2700, retro_rnor_2934,
Ictidomys tridecemlineatus ENSSTOG000000278938 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,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .14 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .14 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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





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