RetrogeneDB ID:

retro_hsap_3958

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:57500965..57501256(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000241431
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL37
Ensembl ID:ENSG00000145592
Aliases:None
Description:ribosomal protein L37 [Source:HGNC Symbol;Acc:10347]


Retrocopy-Parental alignment summary:






>retro_hsap_3958
ATGATGAAGGGAACGTCATCATTTGGAAAGCATTGCAATAAGACGTACACGTTATGCCACCACTGTGGCTCTAAGGCCTA
CCACCTTCAGAAGTCGACCTATGGCAAATGTGGCTACACTGCCAAGCGCAAGAGAAAGTATAACTGGAGTACCAAGGCTA
AAAGACGAAATACCACCAGAACTGGTCAAATGAGGCACCTAAAAATTGTATACCATAGATTCAGGCATGGATTCCGTGAA
GGAACAACACCTAAACCCAAGAGGGCAGCTGTTGCAGCATCCAGTTCATCT

ORF - retro_hsap_3958 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.63 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMTKGTSSFGKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSAKAKRRNTTGTGRMRHLKIV
M.KGTSSFGK..NKT.TLC..CGSKAYHLQKST.GKCGY.AKRKRKYNWS.KAKRRNTT.TG.MRHLKIV
RetrocopyMMKGTSSFGKHCNKTYTLCHHCGSKAYHLQKSTYGKCGYTAKRKRKYNWSTKAKRRNTTRTGQMRHLKIV
ParentalYRRFRHGFREGTTPKPKRAAVAASSSS
Y.RFRHGFREGTTPKPKRAAVAASSSS
RetrocopyYHRFRHGFREGTTPKPKRAAVAASSSS

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 .10 RPM 379 .97 RPM
bodymap2_adrenal 0 .00 RPM 602 .62 RPM
bodymap2_brain 0 .02 RPM 199 .19 RPM
bodymap2_breast 0 .16 RPM 316 .95 RPM
bodymap2_colon 0 .08 RPM 431 .48 RPM
bodymap2_heart 0 .00 RPM 114 .35 RPM
bodymap2_kidney 0 .00 RPM 162 .88 RPM
bodymap2_liver 0 .00 RPM 154 .67 RPM
bodymap2_lung 0 .02 RPM 449 .12 RPM
bodymap2_lymph_node 0 .05 RPM 528 .89 RPM
bodymap2_ovary 0 .04 RPM 616 .36 RPM
bodymap2_prostate 0 .00 RPM 551 .37 RPM
bodymap2_skeletal_muscle 0 .04 RPM 417 .43 RPM
bodymap2_testis 0 .26 RPM 270 .37 RPM
bodymap2_thyroid 0 .00 RPM 265 .52 RPM
bodymap2_white_blood_cells 0 .00 RPM 595 .52 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3958 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3958 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_185447524 libraries443 libraries161 libraries262 libraries439 libraries

The graphical summary, for retro_hsap_3958 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_3958 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3958 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2687
Gorilla gorilla retro_ggor_2660
Pongo abelii retro_pabe_3260
Parental genes homology:
Parental genes homology involve 11 parental genes, and 117 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000145592 21 retrocopies
retro_hsap_1277, retro_hsap_1424, retro_hsap_156, retro_hsap_1747, retro_hsap_1763, retro_hsap_2009, retro_hsap_2120, retro_hsap_2239, retro_hsap_2265, retro_hsap_2499, retro_hsap_2515, retro_hsap_2923, retro_hsap_343, retro_hsap_3610, retro_hsap_3901, retro_hsap_3958 , retro_hsap_4685, retro_hsap_537, retro_hsap_795, retro_hsap_887, retro_hsap_953,
Latimeria chalumnae ENSLACG000000027871 retrocopy
retro_lcha_6,
Loxodonta africana ENSLAFG0000003005213 retrocopies
retro_lafr_1101, retro_lafr_1123, retro_lafr_1125, retro_lafr_1136, retro_lafr_215, retro_lafr_374, retro_lafr_448, retro_lafr_507, retro_lafr_532, retro_lafr_619, retro_lafr_775, retro_lafr_985, retro_lafr_986,
Myotis lucifugus ENSMLUG0000000156510 retrocopies
retro_mluc_1037, retro_mluc_1334, retro_mluc_1441, retro_mluc_1651, retro_mluc_1897, retro_mluc_1917, retro_mluc_2006, retro_mluc_454, retro_mluc_738, retro_mluc_959,
Macaca mulatta ENSMMUG000000238076 retrocopies
retro_mmul_1602, retro_mmul_1672, retro_mmul_206, retro_mmul_329, retro_mmul_976, retro_mmul_997,
Monodelphis domestica ENSMODG000000203013 retrocopies
retro_mdom_130, retro_mdom_1843, retro_mdom_942,
Nomascus leucogenys ENSNLEG000000165084 retrocopies
retro_nleu_1841, retro_nleu_2065, retro_nleu_2407, retro_nleu_77,
Otolemur garnettii ENSOGAG000000343007 retrocopies
retro_ogar_127, retro_ogar_1308, retro_ogar_1662, retro_ogar_1667, retro_ogar_2670, retro_ogar_662, retro_ogar_76,
Pongo abelii ENSPPYG0000001542226 retrocopies
retro_pabe_1058, retro_pabe_1180, retro_pabe_1443, retro_pabe_1532, retro_pabe_1643, retro_pabe_1705, retro_pabe_1756, retro_pabe_1840, retro_pabe_1851, retro_pabe_1865, retro_pabe_1951, retro_pabe_1967, retro_pabe_1985, retro_pabe_212, retro_pabe_2403, retro_pabe_2432, retro_pabe_2962, retro_pabe_3180, retro_pabe_3260, retro_pabe_353, retro_pabe_3549, retro_pabe_3638, retro_pabe_466, retro_pabe_634, retro_pabe_707, retro_pabe_813,
Pan troglodytes ENSPTRG0000001682220 retrocopies
retro_ptro_1208, retro_ptro_1219, retro_ptro_1338, retro_ptro_1451, retro_ptro_1460, retro_ptro_152, retro_ptro_1552, retro_ptro_1584, retro_ptro_1605, retro_ptro_1978, retro_ptro_2440, retro_ptro_2654, retro_ptro_2687, retro_ptro_273, retro_ptro_403, retro_ptro_553, retro_ptro_613, retro_ptro_660, retro_ptro_873, retro_ptro_974,
Rattus norvegicus ENSRNOG000000125386 retrocopies
retro_rnor_171, retro_rnor_181, retro_rnor_220, retro_rnor_246, retro_rnor_321, retro_rnor_325,

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 = 0.15 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .10 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .15 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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



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