RetrogeneDB ID:

retro_hsap_1702

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:72038938..72040220(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000263232
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP5A1
Ensembl ID:ENSG00000152234
Aliases:ATP5A1, ATP5A, ATP5AL2, ATPM, HEL-S-123m, MC5DN4, MOM2, OMR, ORM, hATP1
Description:ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle [Source:HGNC Symbol;Acc:823]


Retrocopy-Parental alignment summary:






>retro_hsap_1702
AAGGAAGGAGGTATAGTGAAGAGGACAGGAACCATTGTGGACGTTCCAGTCGGTGAGGAGCTGTTGGGTCGTGTAGTTGA
TGCCCTTGGTAATGCTATTGATGGAAAGGGTCCAATGGGTTCCAAGACCCATAAGTGAGTCGGTCTGAAAGCCCCCAGAA
TCATTCCTCGAACTTCAGTGTGGGAACCAATGCCGACTGGCATTAAGGCTGTGGATAGCTTGGTGCCAATTGGTCGTGGT
CAGCATGAGCTCATTATTGGTGACCGAAGGACTGGGAAAACCTCAATTGCTATTGACACAATCATTAACCAGAAACATTT
CAATGATAGATCTGAAGAAAAGAAGAAGCTGTACTGTATCTATGTTGCTATTGGTCGAAAGAGATCCACTGTTGCTCAGT
TGGTGAAGAGACTTACAGATGCAGATGCCGTGAAGTACACCACTGTGGTGTCAGCTATGGCCTCAGATGCTGCCCTACTT
CAGTACCTGGCTCCTTACTCTGACTGTTCCATGGGAGAGTATTTTAGAGACGATGGCAAATATACTTTGATCATCTATGA
CGACTTATCCAAACAGGCTGTCGCTTACTGTCAGATGTCTCTGTTGCTCCACCGACCCCCCTGGTCGTAAGGCCTGTCCT
GGTGATGTGTTTTACCTATACTCCCGGTTGCTGGAGAGAGCAGCCAAAATGAATGATGCTTTTGGTGGTGGCTCCTTGAC
TGCTTTGCTAGTCATAGAAACACAGGCCGATGATGTGTCTGCTTACATTCCAACAAATGTCATTTCCATCACTGACAGAC
AGATCTTGGAAACAGAATTGTTCTACAAAGATATCCGCTCTGCCATTAACATTGGGTCTGTCTGTGTCTTGTGTTGGATC
TGCTGCCCAAACCAGGACTATGAAGCAGGCGGCAGGTACCATGAAGCTGGAATTGGCTCAGGATCGTGAGGTTGCTGCTT
TTGCCCAGTTTGGTTCTGACCTCAATGCTCCCACTCAACAACTATTGAGTCGCGGTGTGCGTCTAACTGAGTTGCTGAAG
CAAGGACAGTATCCTCCCATGGTTACTGAACAACAAGTGGCTGTTATCTGTGCGGGTGTAAGGGGGTATCTTGATAAACT
GGAGCCCAGCAAGATTACAAAGTTTGAGAATGCTTTCTTGTCTCATGTTGTCAGCCAGCGCTAAGCCCTGTTGGGCACTA
TCAGGGCTGATGGAAAGATCTCAGAAGACTCAGATGCAAAGCTGATGGAGTTGTAACAAATTTCTTGGCTGGATTTGAAG
CT

ORF - retro_hsap_1702 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.24 %
Parental protein coverage: 77.4 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKTRRRVGLKAPGIIPRISVREPMQTGIKA
KEG.IVKRTG.IVDVPVGEELLGRVVDALGNAIDGKGP.GSKT...VGLKAP.IIPR.SV.EPM.TGIKA
RetrocopyKEGGIVKRTGTIVDVPVGEELLGRVVDALGNAIDGKGPMGSKTHK*VGLKAPRIIPRTSVWEPMPTGIKA
ParentalVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGSDEKKKLYCIYVAIGQKRSTVAQLVKRLTD
VDSLVPIGRGQ.ELIIGDR.TGKTSIAIDTIINQK.FND.S.EKKKLYCIYVAIG.KRSTVAQLVKRLTD
RetrocopyVDSLVPIGRGQHELIIGDRRTGKTSIAIDTIINQKHFNDRSEEKKKLYCIYVAIGRKRSTVAQLVKRLTD
ParentalADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRR-PPGR
ADA.KYT.VVSA.ASDAA.LQYLAPYS.CSMGEYFRD.GK..LIIYDDLSKQAVAY.QMSLLL.R.PPGR
RetrocopyADAVKYTTVVSAMASDAALLQYLAPYSDCSMGEYFRDDGKYTLIIYDDLSKQAVAYCQMSLLLHR>PPGR
ParentalEAYPGDVFYLHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGI
.A.PGDVFYL.SRLLERAAKMNDAFGGGSLTAL.VIETQA.DVSAYIPTNVISITD.QI.LETELFYK.I
RetrocopyKACPGDVFYLYSRLLERAAKMNDAFGGGSLTALLVIETQADDVSAYIPTNVISITDRQI-LETELFYKDI
ParentalRPAINV-GLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQ
R.AIN..GLSVS.VGSAAQTR.MKQ.AGTMKLELAQ.REVAAFAQFGSDL.A.TQQLLSRGVRLTELLKQ
RetrocopyRSAINI>GLSVSCVGSAAQTRTMKQAAGTMKLELAQDREVAAFAQFGSDLNAPTQQLLSRGVRLTELLKQ
ParentalGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVVSQHQALLGTIRADGKISEQSDAKLKE-
GQY.PM..E.QVAVI.AGVRGYLDKLEPSKITKFENAFLSHVVSQ..ALLGTIRADGKISE.SDAKL.E.
RetrocopyGQYPPMVTEQQVAVICAGVRGYLDKLEPSKITKFENAFLSHVVSQR*ALLGTIRADGKISEDSDAKLME<
ParentalIVTNFLAGFEA
.VTNFLAGFEA
RetrocopyVVTNFLAGFEA

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 .04 RPM 212 .28 RPM
bodymap2_adrenal 0 .12 RPM 306 .12 RPM
bodymap2_brain 0 .05 RPM 382 .12 RPM
bodymap2_breast 0 .02 RPM 379 .17 RPM
bodymap2_colon 0 .00 RPM 264 .73 RPM
bodymap2_heart 0 .13 RPM 1310 .46 RPM
bodymap2_kidney 0 .00 RPM 642 .93 RPM
bodymap2_liver 0 .11 RPM 293 .89 RPM
bodymap2_lung 0 .07 RPM 186 .64 RPM
bodymap2_lymph_node 0 .35 RPM 269 .70 RPM
bodymap2_ovary 0 .10 RPM 302 .42 RPM
bodymap2_prostate 0 .03 RPM 350 .44 RPM
bodymap2_skeletal_muscle 0 .04 RPM 405 .73 RPM
bodymap2_testis 0 .13 RPM 310 .02 RPM
bodymap2_thyroid 0 .21 RPM 461 .18 RPM
bodymap2_white_blood_cells 0 .00 RPM 342 .47 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1702 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1702 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1702 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1702 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1702 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1151
Gorilla gorilla retro_ggor_1275
Pongo abelii retro_pabe_1363
Parental genes homology:
Parental genes homology involve 17 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000025072 retrocopies
retro_btau_1380, retro_btau_1426,
Canis familiaris ENSCAFG000000176482 retrocopies
retro_cfam_1483, retro_cfam_516,
Dasypus novemcinctus ENSDNOG000000063312 retrocopies
retro_dnov_1740, retro_dnov_2525,
Equus caballus ENSECAG000000215611 retrocopy
retro_ecab_788,
Homo sapiens ENSG00000152234 1 retrocopy
retro_hsap_1702 ,
Gorilla gorilla ENSGGOG000000165601 retrocopy
retro_ggor_1275,
Meleagris gallopavo ENSMGAG000000099631 retrocopy
retro_mgal_14,
Microcebus murinus ENSMICG000000175001 retrocopy
retro_mmur_1210,
Myotis lucifugus ENSMLUG000000098561 retrocopy
retro_mluc_1198,
Macaca mulatta ENSMMUG000000035701 retrocopy
retro_mmul_1208,
Mustela putorius furoENSMPUG000000009231 retrocopy
retro_mputfur_601,
Nomascus leucogenys ENSNLEG000000109731 retrocopy
retro_nleu_1334,
Pongo abelii ENSPPYG000000091301 retrocopy
retro_pabe_1363,
Pan troglodytes ENSPTRG000000099911 retrocopy
retro_ptro_1151,
Sarcophilus harrisii ENSSHAG000000171771 retrocopy
retro_shar_109,
Tarsius syrichta ENSTSYG000000078041 retrocopy
retro_tsyr_1186,
Tursiops truncatus ENSTTRG000000051181 retrocopy
retro_ttru_159,

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

Indel association:

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





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