RetrogeneDB ID:

retro_hsap_1927

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:23750689..23751250(-)
Located in intron of:ENSG00000154611
Retrocopy
information
Ensembl ID:ENSG00000188985
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DHFR
Ensembl ID:ENSG00000228716
Aliases:DHFR, DHFRP1, DYR
Description:dihydrofolate reductase [Source:HGNC Symbol;Acc:2861]


Retrocopy-Parental alignment summary:






>retro_hsap_1927
ATGGTTGGTTCGCTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCAAGAACGGGGACCTGCCCTGGCCACC
GCTCAGGAATGAATTCAGATATTTCCAGAGAATGACCACAACCTCTTCAGTAGAAGGTAAACAGAATCTGGTGATTATGG
GTAAGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAGGGTAGAATTAATTTAGTTCTCAGCAGAGAACTC
AAGGAACCTCCACAAGGAGCTCATTTTCTTTCCAGAAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGC
AAATAAAGTAGACATGGTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAATCACCCAGGCCATCTTAAAC
TATTTGTGACAAGGATCATGCAAGACTTTGAAAGTGACACGTTTTTTCCAGAAATTGATTTGGAGAAATATAAACTTCTG
CCAGAATACCCAGGTGTTCTCTCTGATGTCCAGGAGGAGAAAGGCATTAAGTACAAATTTGAAGTATATGAGAAGAATGA
T

ORF - retro_hsap_1927 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 100. %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKG
MVGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKG
RetrocopyMVGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKG
ParentalRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIM
RINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIM
RetrocopyRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIM
ParentalQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND
QDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND
RetrocopyQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND

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 .02 RPM 5 .11 RPM
bodymap2_adrenal 0 .18 RPM 11 .85 RPM
bodymap2_brain 0 .02 RPM 6 .75 RPM
bodymap2_breast 0 .39 RPM 25 .29 RPM
bodymap2_colon 0 .00 RPM 6 .90 RPM
bodymap2_heart 0 .00 RPM 1 .51 RPM
bodymap2_kidney 0 .06 RPM 4 .55 RPM
bodymap2_liver 0 .00 RPM 6 .25 RPM
bodymap2_lung 0 .00 RPM 1 .99 RPM
bodymap2_lymph_node 0 .02 RPM 7 .80 RPM
bodymap2_ovary 0 .06 RPM 7 .96 RPM
bodymap2_prostate 0 .00 RPM 4 .57 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .07 RPM
bodymap2_testis 0 .08 RPM 12 .14 RPM
bodymap2_thyroid 0 .08 RPM 13 .69 RPM
bodymap2_white_blood_cells 0 .00 RPM 7 .58 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1927 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CZY POLR2A 18:23751649..23752165

EST - click to see more details

15 EST(s) were mapped to retro_hsap_1927 retrocopy
EST ID Start End Identity Match Mis-match Score
AU124075 79924365 79933771 99.3 793 5 778
BE780840 79924427 79933756 99.2 714 2 699
BM719920 79924567 79929765 99.8 485 1 483
BU630686 79924575 79933761 99.9 585 0 582
BU632674 79924575 79933789 100 613 0 611
CA426593 79924567 79933816 99.9 648 0 645
DA151791 79924477 79929726 100 538 0 537
DA495799 79924477 79929759 99.9 570 1 568
DA749111 79924456 79929740 100 573 0 572
DB527254 79924572 79929718 100 435 0 434
DB576293 79924572 79929777 99.8 493 1 491
DB576543 79924572 79929746 99.8 462 1 460
HY219002 79924580 79929731 100 440 0 439
HY226706 79924569 79929734 98.9 449 5 443
HY267568 79924577 79929741 99.8 452 1 450

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_663451252 libraries436 libraries138 libraries3 libraries0 libraries

The graphical summary, for retro_hsap_1927 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_1927 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1927 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000157502 retrocopies
retro_amel_218, retro_amel_842,
Bos taurus ENSBTAG000000076811 retrocopy
retro_btau_351,
Callithrix jacchus ENSCJAG000000195564 retrocopies
retro_cjac_2017, retro_cjac_2298, retro_cjac_2446, retro_cjac_531,
Equus caballus ENSECAG000000268271 retrocopy
retro_ecab_513,
Felis catus ENSFCAG000000267453 retrocopies
retro_fcat_579, retro_fcat_705, retro_fcat_841,
Homo sapiens ENSG00000228716 4 retrocopies
retro_hsap_1927 , retro_hsap_2119, retro_hsap_3602, retro_hsap_6,
Gorilla gorilla ENSGGOG000000223662 retrocopies
retro_ggor_1959, retro_ggor_2429,
Myotis lucifugus ENSMLUG000000122002 retrocopies
retro_mluc_1109, retro_mluc_2577,
Macaca mulatta ENSMMUG0000001828313 retrocopies
retro_mmul_1496, retro_mmul_425, retro_mmul_692, retro_mmul_693, retro_mmul_695, retro_mmul_700, retro_mmul_701, retro_mmul_704, retro_mmul_738, retro_mmul_760, retro_mmul_768, retro_mmul_82, retro_mmul_994,
Monodelphis domestica ENSMODG000000248603 retrocopies
retro_mdom_1685, retro_mdom_604, retro_mdom_703,
Mustela putorius furoENSMPUG000000087041 retrocopy
retro_mputfur_1107,
Mus musculus ENSMUSG000000217071 retrocopy
retro_mmus_3326,
Nomascus leucogenys ENSNLEG000000129893 retrocopies
retro_nleu_1193, retro_nleu_2314, retro_nleu_2631,
Oryctolagus cuniculus ENSOCUG000000051273 retrocopies
retro_ocun_1351, retro_ocun_1640, retro_ocun_650,
Otolemur garnettii ENSOGAG000000253201 retrocopy
retro_ogar_222,
Pongo abelii ENSPPYG000000156002 retrocopies
retro_pabe_2959, retro_pabe_41,
Pan troglodytes ENSPTRG000000170423 retrocopies
retro_ptro_109, retro_ptro_1551, retro_ptro_2988,
Rattus norvegicus ENSRNOG000000135211 retrocopy
retro_rnor_2030,
Sus scrofa ENSSSCG000000141252 retrocopies
retro_sscr_104, retro_sscr_1131,

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 = 1.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .60 RPM
CEU_NA11843 0 .40 RPM
CEU_NA11930 0 .62 RPM
CEU_NA12004 0 .30 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .22 RPM
CEU_NA12760 0 .40 RPM
CEU_NA12827 0 .38 RPM
CEU_NA12872 0 .33 RPM
CEU_NA12873 0 .41 RPM
FIN_HG00183 0 .47 RPM
FIN_HG00277 0 .37 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .42 RPM
FIN_HG00328 0 .31 RPM
FIN_HG00338 0 .32 RPM
FIN_HG00349 0 .74 RPM
FIN_HG00375 0 .51 RPM
FIN_HG00377 0 .23 RPM
FIN_HG00378 0 .47 RPM
GBR_HG00099 0 .32 RPM
GBR_HG00111 0 .19 RPM
GBR_HG00114 0 .47 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .23 RPM
GBR_HG00133 0 .14 RPM
GBR_HG00134 0 .15 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .17 RPM
GBR_HG00143 0 .26 RPM
TSI_NA20512 0 .25 RPM
TSI_NA20513 0 .27 RPM
TSI_NA20518 1 .05 RPM
TSI_NA20532 0 .41 RPM
TSI_NA20538 0 .37 RPM
TSI_NA20756 0 .38 RPM
TSI_NA20765 0 .46 RPM
TSI_NA20771 0 .31 RPM
TSI_NA20786 0 .21 RPM
TSI_NA20798 0 .37 RPM
YRI_NA18870 0 .47 RPM
YRI_NA18907 0 .38 RPM
YRI_NA18916 0 .32 RPM
YRI_NA19093 0 .26 RPM
YRI_NA19099 0 .48 RPM
YRI_NA19114 0 .37 RPM
YRI_NA19118 0 .31 RPM
YRI_NA19213 0 .17 RPM
YRI_NA19214 0 .22 RPM
YRI_NA19223 0 .28 RPM

Indel association:

The presence of retro_hsap_1927 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_1927 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 18:23747804..23751300 41.8 29.55 25.77 70.45 77.27 82.5 92.35 78.57 89.89 85.48 92.86 73.03 76.29 73

Indel #1, located at the genomic coordinates 18:23747804..23751300.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 70.45 % Puerto Ricansfrom Puerto Rico PUR 77.27 % Colombians fromMedellin, Colombia CLM 82.5 % Americans of AfricanAncestry in SW USA ASW 41.8 % Yoruba in Ibadan,Nigeria YRI 29.55 % Luhya in Webuye,Kenya LWK 25.77 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 92.35 % Iberian Populationin Spain IBS 78.57 % British in Englandand Scotland GBR 89.89 % Finnish in Finland FIN 85.48 % Toscani in Italia TSI 92.86 % Han Chinese in Bejing,China CHB 76.29 % Japanese in Tokyo,Japan 73.03 % Southern Han Chinese CHS 73 % JPT EUROPE AMERICAS AFRICA EAST ASIA




Copyright © RetrogeneDB 2014-2017