RetrogeneDB ID:

retro_hsap_2694

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:120025612..120026799(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000240882
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PTOV1
Ensembl ID:ENSG00000104960
Aliases:PTOV1, ACID2, PTOV-1
Description:prostate tumor overexpressed 1 [Source:HGNC Symbol;Acc:9632]


Retrocopy-Parental alignment summary:






>retro_hsap_2694
GGGACCCCCTCGCGGCCCCTCATAGTGCGCGCTGTCCGCTCCCGCTCCTGGCCAGCCAGCCCCCGAGGCCCGCAGTCTCT
GCAGATCCGGGCCTGCTCGGCCCCTCCCGTGGAAGGTGCTCTTGTCTTCGGGGCGCTGGGTCCCATCGGTCCCTCCTCAC
CTGGGCTCACCCTCGGGGGCCTGGCCGTGAGCGAGCACCGGCTCAGCAACAGGCTGCTGGCCTGGAGCGGCGTCCTCGAG
TGACAGGAGAAGCGCAGACCCTACTGTGACTCCACTATAAAGTTGAGGCGGACCCTGCCCCGCCAAGCCTACGTGAACCA
AGGCGAGAACCTGGAGACCAACCAGTGGCAGCAGAAGCTGATCATGCAGCTGATCCCGCAGCAGCTGATGACCACCCTGG
GACCCCTGTTCCGCAACTCCCGGCTGGCACAGTTCCACTTCACTAACCGAGACTGCTGCTTGCTCAGTGGGCTCTGCCGC
ATCATGGGCAACGGCTTCGCGGGCTGCACGCTGTTTCCCCACATCTCCCCCTGCGAGATGTGCGTGCGCATGCTCCTGTA
CTCTTCCAAGAGGAAGATCTTCATGGGCTTCATCCCCTACGACCAGAGCGGCTTCGTCAGCGCCATCCGGCAGGTCATCA
CTACTCGCAAGCAAGCAGTGGGACCTGGTAGTGTCAACTCAGGCCCAGTCCAGATCGTCAACAACAAGTTCCTGGTGTGG
AGAGGCGTCATGGAGTGGCAGGAACCCAGGCCTGAGCCCAAAAGTCGATCCAAGAGGTGGCTGCCGTCCCACGTCTACGT
GAACCAGGGGGAGATCATGAGGACCGACCAGTGGCCGAGGAAGCTGTAAATGCAGCTCATCCCGCAGCAGCTGCTGACCA
CCCTGTGCTGCTGTTGCGGAACTCGCGCCTGGTGCAGTTCCACTTCACCAAGGACCTGGAGACGCTGAAGAGCCTGTGCC
AGATCAAGGACAATGGCTTCGCCGGCTGAGTGCATTTTTCCTACAAAGTGTTGTGCGAGATCCGCGTGCTCATGCTCCTG
TACTCCTCTGAGAAGAAAATCTTCATCGGCCTCATCCTCCGTGACCAGGGCAACTTCCTCAACGGCATACGGCAAGTCAT
TGCCTACCAGCAGCAGGTCCTGCAGTGGAACCTGGAGCAGGAGCAGCAGCAGCAAGGAATGGAGGGT

ORF - retro_hsap_2694 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.15 %
Parental protein coverage: 95.19 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGRPPRPLVVRAVRSRSWPASPRGPQPPRIRARSAPPMEGARVFGALGPIGPSSPGLTLGGLAVSEHRLSN
G.P.RPL.VRAVRSRSWPASPRGPQ...IRA.SAPP.EGA.VFGALGPIGPSSPGLTLGGLAVSEHRLSN
RetrocopyGTPSRPLIVRAVRSRSWPASPRGPQSLQIRACSAPPVEGALVFGALGPIGPSSPGLTLGGLAVSEHRLSN
ParentalKLLAWSGVLEWQEKRRPYSDSTAKLKRTLPCQAYVNQGENLETDQWPQKLIMQLIPQQLLTTLGPLFRNS
.LLAWSGVLE.QEKRRPY.DST.KL.RTLP.QAYVNQGENLET.QW.QKLIMQLIPQQL.TTLGPLFRNS
RetrocopyRLLAWSGVLE*QEKRRPYCDSTIKLRRTLPRQAYVNQGENLETNQWQQKLIMQLIPQQLMTTLGPLFRNS
ParentalQLAQFHFTNRDCDSLKGLCRIMGNGFAGCMLFPHISPCEVRVLMLLYSSKKKIFMGLIPYDQSGFVSAIR
.LAQFHFTNRDC..L.GLCRIMGNGFAGC.LFPHISPCE..V.MLLYSSK.KIFMG.IPYDQSGFVSAIR
RetrocopyRLAQFHFTNRDCCLLSGLCRIMGNGFAGCTLFPHISPCEMCVRMLLYSSKRKIFMGFIPYDQSGFVSAIR
ParentalQVITTRKQAVGPGGVNSGPVQIVNNKFLAWSGVMEWQEPRPEPNSRSKRWLPSHVYVNQGEILRTEQWPR
QVITTRKQAVGPG.VNSGPVQIVNNKFL.W.GVMEWQEPRPEP.SRSKRWLPSHVYVNQGEI.RT.QWPR
RetrocopyQVITTRKQAVGPGSVNSGPVQIVNNKFLVWRGVMEWQEPRPEPKSRSKRWLPSHVYVNQGEIMRTDQWPR
ParentalKLYMQLIPQQLLTTL-VPLFRNSRLVQFHFTKDLETLKSLCRIMDNGFAGCVHFSYKASCEIRVLMLLYS
KL.MQLIPQQLLTTL.V.L.RNSRLVQFHFTKDLETLKSLC.I.DNGFAG.VHFSYK..CEIRVLMLLYS
RetrocopyKL*MQLIPQQLLTTL<VLLLRNSRLVQFHFTKDLETLKSLCQIKDNGFAG*VHFSYKVLCEIRVLMLLYS
ParentalSEKKIFIGLIPHDQGNFVNGIRRVIANQQQVLQRNLEQEQQQRGMGG
SEKKIFIGLI..DQGNF.NGIR.VIA.QQQVLQ.NLEQEQQQ.GM.G
RetrocopySEKKIFIGLILRDQGNFLNGIRQVIAYQQQVLQWNLEQEQQQQGMEG

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 35 .30 RPM
bodymap2_adrenal 0 .00 RPM 42 .66 RPM
bodymap2_brain 0 .00 RPM 35 .32 RPM
bodymap2_breast 0 .06 RPM 28 .93 RPM
bodymap2_colon 0 .00 RPM 47 .93 RPM
bodymap2_heart 0 .00 RPM 16 .12 RPM
bodymap2_kidney 0 .10 RPM 39 .42 RPM
bodymap2_liver 0 .00 RPM 21 .76 RPM
bodymap2_lung 0 .00 RPM 40 .72 RPM
bodymap2_lymph_node 0 .00 RPM 79 .47 RPM
bodymap2_ovary 0 .00 RPM 68 .80 RPM
bodymap2_prostate 0 .07 RPM 53 .71 RPM
bodymap2_skeletal_muscle 0 .00 RPM 48 .85 RPM
bodymap2_testis 0 .02 RPM 85 .42 RPM
bodymap2_thyroid 0 .00 RPM 55 .51 RPM
bodymap2_white_blood_cells 0 .04 RPM 13 .88 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2694 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2694 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2694 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2694 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2694 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1818
Gorilla gorilla retro_ggor_1877
Pongo abelii retro_pabe_2288
Macaca mulatta retro_mmul_1426
Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000034951 retrocopy
retro_cfam_289,
Callithrix jacchus ENSCJAG000000041051 retrocopy
retro_cjac_445,
Homo sapiens ENSG00000104960 1 retrocopy
retro_hsap_2694 ,
Gorilla gorilla ENSGGOG000000101821 retrocopy
retro_ggor_1877,
Macaca mulatta ENSMMUG000000116181 retrocopy
retro_mmul_1426,
Nomascus leucogenys ENSNLEG000000053741 retrocopy
retro_nleu_1191,
Pongo abelii ENSPPYG000000102651 retrocopy
retro_pabe_2288,
Pan troglodytes ENSPTRG000000113211 retrocopy
retro_ptro_1818,

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 = 0.09 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 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 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .08 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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



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