RetrogeneDB ID:

retro_hsap_1234

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:107315784..107316192(+)
Located in intron of:ENSG00000230156
Retrocopy
information
Ensembl ID:ENSG00000227590
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP5G1
Ensembl ID:ENSG00000159199
Aliases:ATP5G1, ATP5A, ATP5G
Description:ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9) [Source:HGNC Symbol;Acc:841]


Retrocopy-Parental alignment summary:






>retro_hsap_1234
ATGCAGACCACAGGGGCATTACTCATTTCTCCAGCTTGGAACCTCTGTTGTACCTGGGGTCTAATCAGGACTGTATCTGC
CTCCTTCTTGAATAGCCCAGATAATTCACCTAAACAGCCTTCCTACAGCAGCTCCCCACTGCGGGTGGCCAGACGGGAGT
TCCAGACCAGTATTGTCTCCCGGGACATTGACATAGCAGCCAAGTTGATTGGTGCTGGGGCAGCCACAGTTGGTGTGGCT
GGTTCAGGGGCTGGCATTGGAAAAGTGTTTGGCAGCTTGATCATTGGCTATGCCAGGAACCTGTCTCTCAAGCAGCAGCT
CTTCTCCTATGCCACTCTAGGCTTTGCCCTATCTGAGGCCATGGGGCTCTTCTGTTGAATGACCACCTTCCTCATCCTCT
TTGTCATG

ORF - retro_hsap_1234 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.82 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMQTAGALFISPALIRCCTRGLIRPVSASFLNSPVNSSKQPSYSNFPLQVARREFQTSVVSRDIDTAAKFI
MQT.GAL.ISPA...CCT.GLIR.VSASFLNSP.NS.KQPSYS..PL.VARREFQTS.VSRDID.AAK.I
RetrocopyMQTTGALLISPAWNLCCTWGLIRTVSASFLNSPDNSPKQPSYSSSPLRVARREFQTSIVSRDIDIAAKLI
ParentalGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM
GAGAATVGVAGSGAGIG.VFGSLIIGYARN.SLKQQLFSYA.LGFALSEAMGLFC.M..FLILF.M
RetrocopyGAGAATVGVAGSGAGIGKVFGSLIIGYARNLSLKQQLFSYATLGFALSEAMGLFC*MTTFLILFVM

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 .00 RPM 15 .84 RPM
bodymap2_adrenal 0 .00 RPM 32 .22 RPM
bodymap2_brain 0 .00 RPM 30 .03 RPM
bodymap2_breast 0 .00 RPM 17 .45 RPM
bodymap2_colon 0 .00 RPM 24 .11 RPM
bodymap2_heart 0 .00 RPM 111 .15 RPM
bodymap2_kidney 0 .00 RPM 68 .76 RPM
bodymap2_liver 0 .00 RPM 31 .83 RPM
bodymap2_lung 0 .25 RPM 16 .75 RPM
bodymap2_lymph_node 0 .00 RPM 20 .56 RPM
bodymap2_ovary 0 .00 RPM 23 .09 RPM
bodymap2_prostate 0 .00 RPM 31 .18 RPM
bodymap2_skeletal_muscle 0 .00 RPM 33 .30 RPM
bodymap2_testis 0 .00 RPM 19 .97 RPM
bodymap2_thyroid 0 .00 RPM 46 .25 RPM
bodymap2_white_blood_cells 0 .00 RPM 17 .15 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1234 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1234 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_31195529 libraries610 libraries614 libraries72 libraries4 libraries

The graphical summary, for retro_hsap_1234 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_1234 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1234 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_847
Gorilla gorilla retro_ggor_967
Pongo abelii retro_pabe_1027
Parental genes homology:
Parental genes homology involve 20 parental genes, and 87 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000063411 retrocopy
retro_acar_9,
Canis familiaris ENSCAFG000000168805 retrocopies
retro_cfam_1583, retro_cfam_1621, retro_cfam_1882, retro_cfam_336, retro_cfam_647,
Callithrix jacchus ENSCJAG000000073527 retrocopies
retro_cjac_1190, retro_cjac_1549, retro_cjac_161, retro_cjac_1878, retro_cjac_289, retro_cjac_4060, retro_cjac_679,
Cavia porcellus ENSCPOG000000090172 retrocopies
retro_cpor_43, retro_cpor_550,
Equus caballus ENSECAG000000199081 retrocopy
retro_ecab_463,
Felis catus ENSFCAG000000023442 retrocopies
retro_fcat_1165, retro_fcat_1346,
Homo sapiens ENSG000001353906 retrocopies
retro_hsap_1332, retro_hsap_2195, retro_hsap_2703, retro_hsap_3782, retro_hsap_4813, retro_hsap_499,
Homo sapiens ENSG00000159199 8 retrocopies
retro_hsap_1054, retro_hsap_1234 , retro_hsap_1397, retro_hsap_1464, retro_hsap_2844, retro_hsap_2882, retro_hsap_597, retro_hsap_686,
Gorilla gorilla ENSGGOG000000016268 retrocopies
retro_ggor_1083, retro_ggor_1125, retro_ggor_1388, retro_ggor_1998, retro_ggor_528, retro_ggor_589, retro_ggor_831, retro_ggor_967,
Loxodonta africana ENSLAFG000000045372 retrocopies
retro_lafr_341, retro_lafr_522,
Macropus eugenii ENSMEUG000000057442 retrocopies
retro_meug_1650, retro_meug_1973,
Myotis lucifugus ENSMLUG000000117384 retrocopies
retro_mluc_1276, retro_mluc_1508, retro_mluc_1885, retro_mluc_2498,
Macaca mulatta ENSMMUG000000133951 retrocopy
retro_mmul_173,
Mustela putorius furoENSMPUG000000153413 retrocopies
retro_mputfur_1575, retro_mputfur_479, retro_mputfur_497,
Nomascus leucogenys ENSNLEG000000027186 retrocopies
retro_nleu_1082, retro_nleu_1475, retro_nleu_2074, retro_nleu_2219, retro_nleu_623, retro_nleu_777,
Pongo abelii ENSPPYG000000089099 retrocopies
retro_pabe_1027, retro_pabe_1156, retro_pabe_1576, retro_pabe_1607, retro_pabe_2353, retro_pabe_2387, retro_pabe_537, retro_pabe_593, retro_pabe_879,
Pan troglodytes ENSPTRG000000093648 retrocopies
retro_ptro_1273, retro_ptro_1926, retro_ptro_1950, retro_ptro_440, retro_ptro_491, retro_ptro_718, retro_ptro_847, retro_ptro_960,
Rattus norvegicus ENSRNOG000000072355 retrocopies
retro_rnor_1342, retro_rnor_2240, retro_rnor_529, retro_rnor_64, retro_rnor_880,
Ictidomys tridecemlineatus ENSSTOG000000134042 retrocopies
retro_itri_1604, retro_itri_560,
Tupaia belangeri ENSTBEG000000035755 retrocopies
retro_tbel_2765, retro_tbel_3270, retro_tbel_3540, retro_tbel_387, retro_tbel_4002,

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 = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 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 .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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