RetrogeneDB ID:

retro_hsap_3854

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:57216335..57217855(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235095
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GPCPD1
Ensembl ID:ENSG00000125772
Aliases:GPCPD1, GDE5, GDPD6, PREI4
Description:glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26957]


Retrocopy-Parental alignment summary:






>retro_hsap_3854
AGCATGTTATGGAAAGCAACCATTGTACTCAGTAGAGGAGTATCAGTTCAGCATTGCTACTTCAAAGGGTACTTTTTAGA
ACCAAAGACTATCGGTGGTCCATGTCAAGTGATAGTTCACAAGTGGGAGACTCATCTACAACCACGATCAATAACCCCGT
TAGAAAGTGAAATTGTTATTGACCATGGACAATTTGGAATCCACAGTGGTGTTGAAACTCTGGATTCTGCATGGCTGGCA
TGTCAGACTGAAATAAGATTACGATTGCATTATTCTGAAAAACCTCCTGTGTCAATAACCAAGAAAAAATTTTAAAAATC
TAGATTTAGGGTGAAGCTGACACTAGAGGGCCTGGAGGAAGATGAGGATGATAGGGTATCTCCCACTGTACTTCACAAAA
TGTCCAATAGCATGGAGATATCCTTAATATGTGACAATGAGTTCCAGTGCAGGCATTCACAGCTGGAGTGTGGTTATGGC
TTACAGTCTGATCGTTGGACAGAGTACAGCATACAGACAATGGGACCAGATAACCTGGAACTAATCTTTGATTTTTTTGA
AGAAGATCTCAGTGAGCACATAGTTCAAGGTGATGCCCTCCCTGGATGTGTGGGTACAGCTTGTCTCTTATCATCCACCA
TTGCTGAGAGTGGAAAGAGTGCTGGAATTCTTACTCTTCCCATCATGAGCAGAAATTCCAGGAAAACAATAGGCAAAGTG
AGAGTTGACTATATAATTATTAAGCCATTGCCAGGATACAGTTGTGACATGAAATCTTCATTTTCCAGTATTGGAAGCCA
AGAATACCATTGGATGTTGGCCATCGAGGTGTGGGAAACGCTACAACTGCCCAGCTGGCTAAAGAAAATACTATTGCTTC
TTTAAGAAATGCTGCTAGTCACGGTGCAGCCTTTGTAGAATTTGATGTACACCTTTCAAAGGACTTTGTGCCCATGGTAT
ATCATGATCTTACCTGTTGTTTGACTATGAAAAAGAAATTTGATGCTGATCCAGTTGAATTATTTGAAATTCCAGTAAAA
AAAATTAACATTTGACCATCTCCAGTTGTTAAAGCTCACTCATGTGACTGCACTGAAATCTAAGGATTGGAAAGAATCTG
TGGTCCAGGAGGAAAATTCCTTTTCAGAAAATCAGGCATTTCCTTCTCGTAAGATGGTTTTAGAGTGTTTGCCAGAAGAT
GTAGGGTTTAACATTGAAATAAAATGGATCTGCCAGCAAAGGGATGGAATGTGGGATGGTAACTTATCAACATATTTTGG
CATGAATCTGTTTTTGGATATAACTTTAAAAACTGTTTTAGAAAATTCTGGGAAGAGAGAATAGTGTTTTCTTCATTTGA
TGCAGATATTTGCACAATGGTTTGGCAAAGGCAGAACAAATATCCCATATTATTTTTAACTGAAGGAAAATCTGAGATTT
ATCCTGAACTCATGGACCTCAGATCTCCGACAACCCCCATTGCAATGAGCTTTGCACAGTTTGAAAATCTACTAGGGATA

ORF - retro_hsap_3854 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.81 %
Parental protein coverage: 75.89 %
Number of stop codons detected: 1
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalSMLWKATIVLSRGVSVQYRYFKGYFLEPKTIGGPCQVIVHKWETHLQPRSITPLESEIIIDDGQFGIHNG
SMLWKATIVLSRGVSVQ..YFKGYFLEPKTIGGPCQVIVHKWETHLQPRSITPLESEI.ID.GQFGIH.G
RetrocopySMLWKATIVLSRGVSVQHCYFKGYFLEPKTIGGPCQVIVHKWETHLQPRSITPLESEIVIDHGQFGIHSG
ParentalVETLDSGWLTCQTEIRLRLHYSEKPPVSITKKKLKKSRFRVKLTLEGLEEDDDDRVSPTVLHKMSNSLEI
VETLDS.WL.CQTEIRLRLHYSEKPPVSITKKK..KSRFRVKLTLEGLEED.DDRVSPTVLHKMSNS.EI
RetrocopyVETLDSAWLACQTEIRLRLHYSEKPPVSITKKKF*KSRFRVKLTLEGLEEDEDDRVSPTVLHKMSNSMEI
ParentalSLISDNEFKCRHSQPECGYGLQPDRWTEYSIQTMEPDNLELIFDFFEEDLSEHVVQGDALPGHVGTACLL
SLI.DNEF.CRHSQ.ECGYGLQ.DRWTEYSIQTM.PDNLELIFDFFEEDLSEH.VQGDALPG.VGTACLL
RetrocopySLICDNEFQCRHSQLECGYGLQSDRWTEYSIQTMGPDNLELIFDFFEEDLSEHIVQGDALPGCVGTACLL
ParentalSSTIAESGKSAGILTLPIMSRNSRKTIGKVRVDYIIIKPLPGYSCDMKSSFS-KYWKPRIPLDVGHRGAG
SSTIAESGKSAGILTLPIMSRNSRKTIGKVRVDYIIIKPLPGYSCDMKSSFS..YWKPRIPLDVGHRG.G
RetrocopySSTIAESGKSAGILTLPIMSRNSRKTIGKVRVDYIIIKPLPGYSCDMKSSFS<QYWKPRIPLDVGHRGVG
ParentalNSTTTAQLAKVQENTIASLRNAASHGAAFVEFDVHLSKDFVPVVYHDLTCCLTMKKKFDADPVELFEIP-
N..TTAQLAK..ENTIASLRNAASHGAAFVEFDVHLSKDFVP.VYHDLTCCLTMKKKFDADPVELFEIP.
RetrocopyNA-TTAQLAK--ENTIASLRNAASHGAAFVEFDVHLSKDFVPMVYHDLTCCLTMKKKFDADPVELFEIP>
ParentalVKELTFDQLQLLKLTHVTALKSKDRKESVVQEENSFSENQPFPSLKMVLESLPEDVGFNIEIKWICQQRD
...LTFD.LQLLKLTHVTALKSKD.KESVVQEENSFSENQ.FPS.KMVLE.LPEDVGFNIEIKWICQQRD
RetrocopyXXXLTFDHLQLLKLTHVTALKSKDWKESVVQEENSFSENQAFPSRKMVLECLPEDVGFNIEIKWICQQRD
ParentalGMWDGNLSTYFDMNLFLDIILKTVLENSGKR-RIVFSSFDADICTMVRQKQNKYPILFLTQGKSEIYPEL
GMWDGNLSTYF.MNLFLDI.LKTVLENSGKR.RIVFSSFDADICTMV.Q.QNKYPILFLT.GKSEIYPEL
RetrocopyGMWDGNLSTYFGMNLFLDITLKTVLENSGKR<RIVFSSFDADICTMVWQRQNKYPILFLTEGKSEIYPEL
ParentalMDLRSRTTPIAMSFAQFENLLGI
MDLRS.TTPIAMSFAQFENLLGI
RetrocopyMDLRSPTTPIAMSFAQFENLLGI

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 38 .54 RPM
bodymap2_adrenal 0 .00 RPM 78 .81 RPM
bodymap2_brain 0 .00 RPM 47 .82 RPM
bodymap2_breast 0 .02 RPM 59 .44 RPM
bodymap2_colon 0 .00 RPM 26 .78 RPM
bodymap2_heart 0 .00 RPM 16 .45 RPM
bodymap2_kidney 0 .00 RPM 41 .86 RPM
bodymap2_liver 0 .00 RPM 10 .06 RPM
bodymap2_lung 0 .00 RPM 79 .61 RPM
bodymap2_lymph_node 0 .00 RPM 35 .40 RPM
bodymap2_ovary 0 .00 RPM 119 .29 RPM
bodymap2_prostate 0 .00 RPM 68 .22 RPM
bodymap2_skeletal_muscle 0 .04 RPM 36 .12 RPM
bodymap2_testis 0 .11 RPM 35 .48 RPM
bodymap2_thyroid 0 .00 RPM 55 .53 RPM
bodymap2_white_blood_cells 0 .00 RPM 113 .36 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_3854 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3854 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3854 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3854 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3854 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000125772 1 retrocopy
retro_hsap_3854 ,
Pongo abelii ENSPPYG000000106871 retrocopy
retro_pabe_3052,
Pan troglodytes ENSPTRG000000132281 retrocopy
retro_ptro_2625,
Ictidomys tridecemlineatus ENSSTOG000000068271 retrocopy
retro_itri_1811,

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 = 0.08 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 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 .08 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 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 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 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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