RetrogeneDB ID:

retro_hsap_2017

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:19:57686598..57687909(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000268379
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PTCD3
Ensembl ID:ENSG00000132300
Aliases:PTCD3, MRP-S39
Description:pentatricopeptide repeat domain 3 [Source:HGNC Symbol;Acc:24717]


Retrocopy-Parental alignment summary:






>retro_hsap_2017
ATGGCGGCTGTAGCTGCTGTTCGCTGGCTGGGGCTCTGCAGCAGGCTTGACCAGCCACTGACGGGTCAGCCAGCAGGTCT
ATGTGAACAAGCACACAGCTGAGATTTTATTCTGGAAGTGCAACCCTCTCAAATATTGAAGGAACTGATATAACAGGGAT
TGAAGAAGTAGTAATTCCAAAAAAGAAAACTTGGGATAAAGTAGCCGTTCTTCAGGCTCTTGCATCCACAGTAAACAGGG
TTCCCACGGCTGTACCTTGCGTGTTTCAAGATAATCCTTACCTCATACCAACATCCTCTTCAGAATCTCGTTCATTTTTA
CTGGCAAAGAAATCCGGGGAGAATACGGCCAAGTTCATTATTAATTCATACTCCAAATATTTTCAGAAAGACATAGCTGA
ACCTCATACACTGTGTTTAATGCCTGAGTACTTTGAACCTCAGATCAAAGACATAAGTGAAGCCACTCTCAAGGAATGAA
TCAAGCTCAGAAAAGTCAAAGTCTCTGTGGACATGTTTGATGAGCTTTTGCAAGCAGGAACCACTGTGTCTCTTGTAACA
ACATATAGTCTCTTGGATTTATTGTGTTACTATGGTGACCAGGAGCCCTCAACTGATTATCAGTTTCAACAAATTGAACA
GTCAGAAGAATTGGAAGAGGAAAATAATAAGAGGTCTAGGAGGAAAGCTGGTGATCAATTTGGAGTTACCTGGTGAGCAC
AAAACAACGCTGAGAGAATGTTTTCTCTAATGCCAGGGAAAAATGCACATTCCTATTGCACAGTGATCCGAGGAATGGTG
AAGCATCAAGCTTATGAGCAGGCATTAAACCTGTACACTGAGTTACTAAACAACAGACTCTGTGCTGATGTATACACATT
TAATGCAGTGATTGAAGCAACAGTATTGGTGATAAATGAGAAATTTGAGGAAGAATGGAATAATATACTGGAGCTGCTAA
GACAAATGGTTGCACAGAAGGTGAAACCAAATCTACAGACTTTTAATACCATTCTGAAATGTCTCCGAAGATTTTATGTA
CTTGCAAGATTGCCAGCCTTACAGATTCTATGTGAAATGAAAGCCATCAGACTAGAACCCTCGCTTGCAACATATCACCA
TATTATTCAGCTGTTTTATCAGCCTGGAAACCCTTCAAAGGGATCATCTTTCATCATCTATGATATAATGAATGAATTAA
TGGGAAAGAGATTTTCCCCCAAAGGACCTGGATGATGATAAGCTTTTTCAGTCAGCCATGAGAGTATCTTCATCTCTCAG
AAATCTAGAACTTGCGTACCAAATACATGGC

ORF - retro_hsap_2017 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.37 %
Parental protein coverage: 63.43 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAVVSAVRWLGLRSRLGQPLTGRRAGLCEQARS-CRFYSGSATLSKVEGTDVTGIEEVVIPKKKTWDKVA
MA.V.AVRWLGL.SRL.QPLTG..AGLCEQA.S..RFYSGSATLS..EGTD.TGIEEVVIPKKKTWDKVA
RetrocopyMAAVAAVRWLGLCSRLDQPLTGQPAGLCEQAHS<LRFYSGSATLSNIEGTDITGIEEVVIPKKKTWDKVA
ParentalVLQALASTVNRDTTAVPYVFQDDPYLMPASSLESRSFLLAKKSGENVAKFIINSYPKYFQKDIAEPHIPC
VLQALASTVNR..TAVP.VFQD.PYL.P.SS.ESRSFLLAKKSGEN.AKFIINSY.KYFQKDIAEPH..C
RetrocopyVLQALASTVNRVPTAVPCVFQDNPYLIPTSSSESRSFLLAKKSGENTAKFIINSYSKYFQKDIAEPHTLC
ParentalLMPEYFEPQIKDISEAALKERIELRKVKASVDMFDQLLQAGTTVSLETTNSLLDLLCYYGDQEPSTDYHF
LMPEYFEPQIKDISEA.LKE.I.LRKVK.SVDMFD.LLQAGTTVSL.TT.SLLDLLCYYGDQEPSTDY.F
RetrocopyLMPEYFEPQIKDISEATLKE*IKLRKVKVSVDMFDELLQAGTTVSLVTTYSLLDLLCYYGDQEPSTDYQF
ParentalQQTGQSEALEEENDETSRRKAGHQFGVTWRAKNNAERIFSLMPEKNEHSYCTMIRGMVKHRAYEQALNLY
QQ..QSE.LEEEN...SRRKAG.QFGVTW.A.NNAER.FSLMP.KN.HSYCT.IRGMVKH.AYEQALNLY
RetrocopyQQIEQSEELEEENNKRSRRKAGDQFGVTW*AQNNAERMFSLMPGKNAHSYCTVIRGMVKHQAYEQALNLY
ParentalTELLNNRLHADVYTFNALIEATVCAINEKFEEKWSKILELLRHMVAQKVKPNLQTFNTILKCLRRFHVFA
TELLNNRL.ADVYTFNA.IEATV..INEKFEE.W..ILELLR.MVAQKVKPNLQTFNTILKCLRRF.V.A
RetrocopyTELLNNRLCADVYTFNAVIEATVLVINEKFEEEWNNILELLRQMVAQKVKPNLQTFNTILKCLRRFYVLA
ParentalRSPALQVLREMKAIGIEPSLATYHHIIRLFDQPGDPLKRSSFIIYDIMNELMGKRFSPKDP-DDDKFFQS
R.PALQ.L.EMKAI..EPSLATYHHII.LF.QPG.P.K.SSFIIYDIMNELMGKRFSPK.P.DDDK.FQS
RetrocopyRLPALQILCEMKAIRLEPSLATYHHIIQLFYQPGNPSKGSSFIIYDIMNELMGKRFSPKGP>DDDKLFQS
ParentalAMSICSSLRDLELAYQVHG
AM...SSLR.LELAYQ.HG
RetrocopyAMRVSSSLRNLELAYQIHG

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 .18 RPM 18 .53 RPM
bodymap2_adrenal 0 .12 RPM 55 .47 RPM
bodymap2_brain 0 .30 RPM 64 .34 RPM
bodymap2_breast 0 .06 RPM 44 .75 RPM
bodymap2_colon 0 .00 RPM 31 .00 RPM
bodymap2_heart 0 .00 RPM 96 .70 RPM
bodymap2_kidney 0 .29 RPM 66 .45 RPM
bodymap2_liver 0 .00 RPM 40 .47 RPM
bodymap2_lung 0 .12 RPM 29 .54 RPM
bodymap2_lymph_node 0 .00 RPM 54 .35 RPM
bodymap2_ovary 0 .33 RPM 63 .81 RPM
bodymap2_prostate 0 .02 RPM 55 .61 RPM
bodymap2_skeletal_muscle 0 .00 RPM 64 .22 RPM
bodymap2_testis 0 .26 RPM 101 .52 RPM
bodymap2_thyroid 0 .06 RPM 74 .33 RPM
bodymap2_white_blood_cells 0 .02 RPM 39 .14 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2017 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2017 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2017 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2017 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2017 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1461
Pongo abelii retro_pabe_1653
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000132300 1 retrocopy
retro_hsap_2017 ,
Gorilla gorilla ENSGGOG000000017931 retrocopy
retro_ggor_1461,
Nomascus leucogenys ENSNLEG000000024931 retrocopy
retro_nleu_2729,
Pongo abelii ENSPPYG000000122161 retrocopy
retro_pabe_1653,

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 = 0.23 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 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 .13 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .10 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .17 RPM
GBR_HG00131 0 .23 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .17 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .15 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 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 .05 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .07 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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