RetrogeneDB ID:

retro_hsap_1120

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:55805508..55808298(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000179899
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PHC1
Ensembl ID:ENSG00000111752
Aliases:PHC1, EDR1, HPH1, MCPH11, RAE28
Description:polyhomeotic homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:3182]


Retrocopy-Parental alignment summary:






>retro_hsap_1120
CAGGCCACAATTGCTGCCAGTCGGCAGGCCAGCTCCCCAAACACCAGCACTACACAGCAGCAGACTACCACCACCCAGGC
CTCGATCAATCTGGCCACCACATCGGCCGCCCAGCTCATCAGCCGATCCCAGAGTGTGAGCTCTCCCAGTGCTACCACCT
TGACCCAATCTGTGCTACTGGGGAACACCACCTCCCCACCCCTCAACCAGTCTCAGGCCCAGATGTATCTACGGCCACAG
CTGGGAAACCTATTGCAGGTAAACCGAACCCTGGGTCGGAATGTGCCTCTAGCCTCCCAACTCATCCTGATGCCTAATGG
GGCAGTGGCTGCAGTCCAGCAGGAGGTGCCATCTGCTCAGTCTCCTGGAGTTCATGCAGATGCAGATCAGGTTCAGAACT
TGGCAGTAAGGAATCAACAGGCCTCAGCTCAAGGACCTCAGATGCAAGGCTCCACTCAGAAGGCCATTCCTCCAGGAGCC
TCCCCTGTCTCTAGCCTCTCCCAGGCCTCTAGCCAGGCCCTAGCGGTGGCACAGGCTTCCTCTGGGGCCACAAACCAGTC
CCTCAACCTTAGTCAAGCTGGTGGAGGCAGTGGGAATAGCATCCCAGGGTCCATGGGTCCAGGTGGAGGTGGGCAGGCAC
ATGGTGGTTTGGGTCAGTTGCCTTCCTCAGGAATGGGTGGTGGGAGCTGTCCCAGGAAGGGTACAGGAGTGGTGCAGCCC
TTGCCTGCAGCCCAAACAGTGACTGTGAGCCAGGGCAGCCAGACAGAGGCAGAAAGTGCAGCAGCCAAGAAGGCAGAAGC
AGATGGGAGTGGCCAGCAGAATGTGGGCATGAACCTGACACGGACAGCCACACCTGCGCCCAGCCAGACACTTATTAGCT
CAGCCACCTACACACAGATCCAGCCCCATTCACTGATTCAGCAACAGCAACAGATCCACCTCCAGCAGAAACAGGTGGTG
ATCCAGCAGCAGATTGCCATCCACCACCAGCAGCAGTTCCAGCACTGGCAGTCCCAGCTCCTTCACACAGCTACACACCT
CCAGTTGGCGCAGCAGCAGCAGCAGCAACAACAGCAACAGCAGCAACAGCAGCAGCCGCAAGCCACCACCCTCACTGCCC
CTCAGCCACCACAGGTCCCACCTACTCAGCAGGTCCCACCTTCCCAGTCCCAGCAGCAAGCCCAAACCCTGGTCGTTCAG
CCCATGCTTCAGTCTTCACCCTTGTCTCTTCCACCTGATGCAGCCCCTAAGCCACCAATTCCCATCCAATCCAAACCACC
TGTAGCACCTATCAAGCCGCCTCAGTTAGGGGCCGCTAAGATGTCAGCTGCCCAGCAACCACCACCCCATATCCCTGTGC
AAGTTGTAGGCACTCGACAGCCAGGTACAGCCCAGGCACAGGCTTTGGGGTTGGCACAGCTGGCAGCTGCTGTACCTACT
TCCCGGGGGATGCCAGGTACAGTGCAGTCTGGTCAGGCCCATTTGGCCTCCTCGCCACCTTCATCCCAGGCTCCTGGTGC
ACTGCAGGAGTGCCCTCCCACATTGGCCCCTGGGATGACCCTTGCTCCTGTGCAGGGGACAGCACATGTGGTAAAGGGTG
GGGCTACCACCTCCTCACCTGTTGTAGCCCAGGTCCCTGCTGCCTTCTATATGCAGTCTGTGCACTTGCCGGGTAAACCC
CAGACATTGGCTGTCAAACGCAAGGCTGACTCTGAGGAGGAGAGAGATGATGTCTCCACATTGGGTTCAATGCTTCCTGC
CAAGGCATCTCCAGTAGCAGAAAGCCCAAAAGTCATGGACGAGAAGAGCAGTCTTGGAGAAAAAGCTGAATCAGTGGCTA
ATGTGAATGCTAATACTCCAAACAGTGAACTAGTAGCCTTGACCCCCGCCCCTTCAGTACCGCCTCCTACACTAGCCATG
GTGTCTAGACAAATGGGTGACTCAAAACCCCCACAGGCCATCGTGAAGCCCCAGATTCTCACCCACATCATTGAAGGCTT
TGTTATCCAGGAAGGAGCAGAACCTTTCCCGGTGGGTTGTTCTCAGTTACTGAAGGAGTCTGAGAAGCCACTACAGACTG
GCCTTCCGACAGGGCTGACTGAGAATCAGTCAGGTGGCCCTTTGGGAGTGGACAGCCCATCTGCTGAGTTAGATAAGAAG
GCGAATCTCCTGAAGTGCGAGTACTGTGGGAAGTACGCCCCCGCAGAGCAGTTTCGTGGCTCTAAGAGGTTCTGCTCCAT
GACTTGCGCTAAGAGGTACAATGTGAGCTGTAGCCATCAGTTCCGGCTGAAGAGGAAAAAAATGAAAGAGTTTCAAGAAG
CCAACTATGCTCGCGTTCGCAGGCGTGGACCCCGCCGCAGCTCCTCTGACATTGCCCGTGCCAAGATTCAGGGCAAGTGC
CACCGGGGTCAAGAAGACTCTAGCCGGGGTTCAGATAATTCCAGTTATGATGAAGCACTCTCTCCAACATCTCCTGGGCC
TTTATCAGTAAGAGCTGGGCATGGAGAACGTGACCTGGGGAATCCCAATACAGCTCCACCTACACCGGAATTACATGGCA
TCAACCCTGTGTTCCTGTCCAGTAATCCCAGCCGTTGGAGTGTAGAGGAGGTGTACGAGTTTATTGCTTCTCTCCAAGGC
TGCCAAGAGATTGCAGAGGAATTTCGCTCACAGGAGATTGATGGACAGGCCCTTTTATTACTTAAAGAAGAACATCTTAT
GAGTGCCATGAACATCAAGCTGGGCCCTGCCCTCAAGATCTGCGCCAAGATAAATGTCCTCAAGGAGACC

ORF - retro_hsap_1120 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.85 %
Parental protein coverage: 92.63 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQATIAASRQASSPNTSTTQQQTTTTQASINLATTSAAQLISRSQSVSSPSATTLTQSVLLGNTTSPPLNQ
QATIAASRQASSPNTSTTQQQTTTTQASINLATTSAAQLISRSQSVSSPSATTLTQSVLLGNTTSPPLNQ
RetrocopyQATIAASRQASSPNTSTTQQQTTTTQASINLATTSAAQLISRSQSVSSPSATTLTQSVLLGNTTSPPLNQ
ParentalSQAQMYLRPQLGNLLQVNRTLGRNVPLASQLILMPNGAVAAVQQEVPSAQSPGVHADADQVQNLAVRNQQ
SQAQMYLRPQLGNLLQVNRTLGRNVPLASQLILMPNGAVAAVQQEVPSAQSPGVHADADQVQNLAVRNQQ
RetrocopySQAQMYLRPQLGNLLQVNRTLGRNVPLASQLILMPNGAVAAVQQEVPSAQSPGVHADADQVQNLAVRNQQ
ParentalASAQGPQMQGSTQKAIPPGASPVSSLSQASSQALAVAQASSGATNQSLNLSQAGGGSGNSIPGSMGPGGG
ASAQGPQMQGSTQKAIPPGASPVSSLSQASSQALAVAQASSGATNQSLNLSQAGGGSGNSIPGSMGPGGG
RetrocopyASAQGPQMQGSTQKAIPPGASPVSSLSQASSQALAVAQASSGATNQSLNLSQAGGGSGNSIPGSMGPGGG
ParentalGQAHGGLGQLPSSGMGGGSCPRKGTGVVQPLPAAQTVTVSQGSQTEAESAAAKKAEADGSGQQNVGMNLT
GQAHGGLGQLPSSGMGGGSCPRKGTGVVQPLPAAQTVTVSQGSQTEAESAAAKKAEADGSGQQNVGMNLT
RetrocopyGQAHGGLGQLPSSGMGGGSCPRKGTGVVQPLPAAQTVTVSQGSQTEAESAAAKKAEADGSGQQNVGMNLT
ParentalRTATPAPSQTLISSATYTQIQPHSLIQQQQQIHLQQKQVVIQQQIAIHHQQQFQHRQSQLLHTATHLQLA
RTATPAPSQTLISSATYTQIQPHSLIQQQQQIHLQQKQVVIQQQIAIHHQQQFQH.QSQLLHTATHLQL.
RetrocopyRTATPAPSQTLISSATYTQIQPHSLIQQQQQIHLQQKQVVIQQQIAIHHQQQFQHWQSQLLHTATHLQLX
ParentalQQQQQQQQQQQQQQQPQATTLTAPQPPQVPPTQQVPPSQSQQQAQTLVVQPMLQSSPLSLPPDAAPKPPI
.................ATTLTAPQPPQVPPTQQVPPSQSQQQAQTLVVQPMLQSSPLSLPPDAAPKPPI
RetrocopyXXXXXXXXXXXXXXXXXATTLTAPQPPQVPPTQQVPPSQSQQQAQTLVVQPMLQSSPLSLPPDAAPKPPI
ParentalPIQSKPPVAPIKPPQLGAAKMSAAQQPPPHIPVQVVGTRQPGTAQAQALGLAQLAAAVPTSRGMPGTVQS
PIQSKPPVAPIKPPQLGAAKMSAAQQPPPHIPVQVVGTRQPGTAQAQALGLAQLAAAVPTSRGMPGTVQS
RetrocopyPIQSKPPVAPIKPPQLGAAKMSAAQQPPPHIPVQVVGTRQPGTAQAQALGLAQLAAAVPTSRGMPGTVQS
ParentalGQAHLASSPPSSQAPGALQECPPTLAPGMTLAPVQGTAHVVKGGATTSSPVVAQVPAAFYMQSVHLPGKP
GQAHLASSPPSSQAPGALQECPPTLAPGMTLAPVQGTAHVVKGGATTSSPVVAQVPAAFYMQSVHLPGKP
RetrocopyGQAHLASSPPSSQAPGALQECPPTLAPGMTLAPVQGTAHVVKGGATTSSPVVAQVPAAFYMQSVHLPGKP
ParentalQTLAVKRKADSEEERDDVSTLGSMLPAKASPVAESPKVMDEKSSLGEKAESVANVNANTPSSELVALTPA
QTLAVKRKADSEEERDDVSTLGSMLPAKASPVAESPKVMDEKSSLGEKAESVANVNANTP.SELVALTPA
RetrocopyQTLAVKRKADSEEERDDVSTLGSMLPAKASPVAESPKVMDEKSSLGEKAESVANVNANTPNSELVALTPA
ParentalPSVPPPTLAMVSRQMGDSKPPQAIVKPQILTHIIEGFVIQEGAEPFPVGCSQLLKESEKPLQTGLPTGLT
PSVPPPTLAMVSRQMGDSKPPQAIVKPQILTHIIEGFVIQEGAEPFPVGCSQLLKESEKPLQTGLPTGLT
RetrocopyPSVPPPTLAMVSRQMGDSKPPQAIVKPQILTHIIEGFVIQEGAEPFPVGCSQLLKESEKPLQTGLPTGLT
ParentalENQSGGPLGVDSPSAELDKKANLLKCEYCGKYAPAEQFRGSKRFCSMTCAKRYNVSCSHQFRLKRKKMKE
ENQSGGPLGVDSPSAELDKKANLLKCEYCGKYAPAEQFRGSKRFCSMTCAKRYNVSCSHQFRLKRKKMKE
RetrocopyENQSGGPLGVDSPSAELDKKANLLKCEYCGKYAPAEQFRGSKRFCSMTCAKRYNVSCSHQFRLKRKKMKE
ParentalFQEANYARVRRRGPRRSSSDIARAKIQGKCHRGQEDSSRGSDNSSYDEALSPTSPGPLSVRAGHGERDLG
FQEANYARVRRRGPRRSSSDIARAKIQGKCHRGQEDSSRGSDNSSYDEALSPTSPGPLSVRAGHGERDLG
RetrocopyFQEANYARVRRRGPRRSSSDIARAKIQGKCHRGQEDSSRGSDNSSYDEALSPTSPGPLSVRAGHGERDLG
ParentalNPNTAPPTPELHGINPVFLSSNPSRWSVEEVYEFIASLQGCQEIAEEFRSQEIDGQALLLLKEEHLMSAM
NPNTAPPTPELHGINPVFLSSNPSRWSVEEVYEFIASLQGCQEIAEEFRSQEIDGQALLLLKEEHLMSAM
RetrocopyNPNTAPPTPELHGINPVFLSSNPSRWSVEEVYEFIASLQGCQEIAEEFRSQEIDGQALLLLKEEHLMSAM
ParentalNIKLGPALKICAKINVLKET
NIKLGPALKICAKINVLKET
RetrocopyNIKLGPALKICAKINVLKET

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 1 .05 RPM 6 .78 RPM
bodymap2_adrenal 0 .96 RPM 8 .27 RPM
bodymap2_brain 0 .91 RPM 5 .86 RPM
bodymap2_breast 0 .47 RPM 5 .84 RPM
bodymap2_colon 0 .81 RPM 8 .97 RPM
bodymap2_heart 0 .50 RPM 7 .46 RPM
bodymap2_kidney 0 .17 RPM 8 .33 RPM
bodymap2_liver 0 .00 RPM 0 .80 RPM
bodymap2_lung 0 .25 RPM 8 .56 RPM
bodymap2_lymph_node 0 .57 RPM 15 .31 RPM
bodymap2_ovary 1 .48 RPM 18 .37 RPM
bodymap2_prostate 0 .74 RPM 12 .28 RPM
bodymap2_skeletal_muscle 0 .29 RPM 7 .71 RPM
bodymap2_testis 1 .56 RPM 27 .90 RPM
bodymap2_thyroid 1 .51 RPM 9 .21 RPM
bodymap2_white_blood_cells 0 .12 RPM 5 .91 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1120 was not detected

EST - click to see more details

18 EST(s) were mapped to retro_hsap_1120 retrocopy
EST ID Start End Identity Match Mis-match Score
AA300989 55805664 55805931 99.3 262 1 259
AA338510 55805712 55806002 100 289 0 289
BF759538 55807395 55807810 97.9 406 7 395
BF922901 55807563 55807808 96.7 236 2 228
BI009099 55807568 55807906 98.9 334 4 330
BI752280 55805398 55806223 99.9 822 1 819
BP241296 55805426 55805978 99.5 549 3 546
BQ326716 55807411 55807737 95.7 320 2 307
CN388294 55805645 55806169 100 524 0 524
CN388295 55805657 55806138 100 481 0 481
CN388300 55805890 55806420 100 530 0 530
CN388308 55805877 55806421 100 544 0 544
CT001603 55805594 55806282 100 680 0 680
CX760667 55806447 55806566 99.2 117 1 115
DA609879 55805739 55806294 100 555 0 555
HY270459 55805801 55806274 100 473 0 473
HY306555 55805479 55806004 100 523 0 523
HY310658 55806744 55807255 100 511 0 511

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_268661406 libraries363 libraries53 libraries7 libraries0 libraries

The graphical summary, for retro_hsap_1120 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_1120 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1120 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000111752 1 retrocopy
retro_hsap_1120 ,

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 = 0.86 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .36 RPM
CEU_NA11843 0 .37 RPM
CEU_NA11930 0 .75 RPM
CEU_NA12004 0 .19 RPM
CEU_NA12400 0 .35 RPM
CEU_NA12751 0 .75 RPM
CEU_NA12760 0 .76 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .57 RPM
CEU_NA12873 0 .61 RPM
FIN_HG00183 0 .41 RPM
FIN_HG00277 0 .55 RPM
FIN_HG00315 0 .33 RPM
FIN_HG00321 0 .54 RPM
FIN_HG00328 0 .28 RPM
FIN_HG00338 0 .49 RPM
FIN_HG00349 0 .26 RPM
FIN_HG00375 0 .29 RPM
FIN_HG00377 0 .28 RPM
FIN_HG00378 0 .17 RPM
GBR_HG00099 0 .61 RPM
GBR_HG00111 0 .21 RPM
GBR_HG00114 0 .45 RPM
GBR_HG00119 0 .29 RPM
GBR_HG00131 0 .66 RPM
GBR_HG00133 0 .31 RPM
GBR_HG00134 0 .70 RPM
GBR_HG00137 0 .38 RPM
GBR_HG00142 0 .56 RPM
GBR_HG00143 0 .19 RPM
TSI_NA20512 0 .20 RPM
TSI_NA20513 0 .39 RPM
TSI_NA20518 0 .44 RPM
TSI_NA20532 0 .27 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .46 RPM
TSI_NA20771 0 .51 RPM
TSI_NA20786 0 .86 RPM
TSI_NA20798 0 .28 RPM
YRI_NA18870 0 .61 RPM
YRI_NA18907 0 .21 RPM
YRI_NA18916 0 .29 RPM
YRI_NA19093 0 .57 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .84 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .62 RPM
YRI_NA19214 0 .37 RPM
YRI_NA19223 0 .46 RPM

Indel association:

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





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