RetrogeneDB ID:

retro_hsap_3924

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:158414972..158416153(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000224324
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:THAP5
Ensembl ID:ENSG00000177683
Aliases:None
Description:THAP domain containing 5 [Source:HGNC Symbol;Acc:23188]


Retrocopy-Parental alignment summary:






>retro_hsap_3924
ATGCCCCGCTATTGCGCGGCGATTTGTTGTAAGAACTGCCGGGGATGAAACAATAAAGACCGGAAGCTGAGTTTTTATCC
ATTTCCTCTACATGACAAAGAAAGACTGGAAAAGTGGTTAAACAATATGAAGCGAGATTCATGGGTTCCCAGTAAATACC
AGTTTCTGTGTAGTGACCATTTTACTCCTGACTCTCTTGACATCAGATGGGGTATTCGATATTTAAAACAAAGTGCAGTT
CCAACAATATTTTCTTTGCCTGAAGACAATCAGGGAAAAGACCCTTCTAAAAAAAAATCCCAGAAGAAAAACTTGGAAGA
TGAGAAGTATGCCCAAAAGCCAAGTCAGAAGAATCAGTTGTATTAAATGAGACAAAGAAAAATATAGTTAACACAAATGT
GCTCCCTCAACATCCAGAATTACTTCATTCATCTTCCTTGGTAAAGCCACCAGCTCCCAAAACAGGAAGTATACAAAATA
ACATGTTAACTCTTAATCTAGTTAAACAACATACTGGGAAACCAGAATCTACCTTGGAAACATCAGTTAACCAAGATACA
GGTGTAGGTGGTTTTCACACATGTTTTTATAATCTAAATTCTACAACTATTACTTTGACAATTTCAAATTCAGAAAGTAT
TCATCAATCTTTGGAAACCCAAGAAGTTCTTGAAGTAACTTCTAGTTATCTTGCTAATCCAAACTTTACAAGTAATTCCA
TGGAAATAAAGTCAGCACAGGAAAATCCATTCTTATTCAGCACAATTAAGCAAACAGTTGAAGAATTAAACACAAATAAA
GAATCTGTTATTGCCATTTTTGTACCTGCCAAAAATTCTAAACTTTCAGTTAATTCTTTTATATCTGCACAAAAAGAAAC
CACGGAAGTGGAAGACATAGACATCGAAGACTCCTTGTATAAGGATGTAGACTATGGGACAGAAGTTTTACAAATAGAAC
ATTCTTACTGCAGACAAGATATAAATAAGGAGCATCTTTGGCAGAAAGTCTCTAAGCTACATTCAAAGATAACTCTTCTA
GAGTTCAAAGAGCAACAAACTCTAGGTAGATTGAAGTCTTTGGAAGCTCTTATAAGGCAGCTAAAGCAGGAAAACTGGCT
ATCTGAAGAAAATGTCAAGATCATAGAAAACCGTTTTACAACATATGAAGTCACTATGATA

ORF - retro_hsap_3924 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.16 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPRYCAAICCKNRRGRNNKDRKLSFYPFPLHDKERLEKWLKNMKRDSWVPSKYQFLCSDHFTPDSLDIRW
MPRYCAAICCKN.RG.NNKDRKLSFYPFPLHDKERLEKWL.NMKRDSWVPSKYQFLCSDHFTPDSLDIRW
RetrocopyMPRYCAAICCKNCRG*NNKDRKLSFYPFPLHDKERLEKWLNNMKRDSWVPSKYQFLCSDHFTPDSLDIRW
ParentalGIRYLKQTAVPTIFSLPEDNQ-GKDPSKKKSQKKNLEDEKEVCPKAKSEESFVLNETKKNIVNTDVPHQH
GIRYLKQ.AVPTIFSLPEDNQ.GK.P.........L....EVCPKAKSEES.VLNETKKNIVNT.V..QH
RetrocopyGIRYLKQSAVPTIFSLPEDNQ<GKRPFXXXXPEEKL-GR*EVCPKAKSEESVVLNETKKNIVNTNVLPQH
ParentalPELLHSSSLVKPPAPKTGSIQNNMLTLNLVKQHTGKPESTLETSVNQDTGRGGFHTCFENLNSTTITLTT
PELLHSSSLVKPPAPKTGSIQNNMLTLNLVKQHTGKPESTLETSVNQDTG.GGFHTCF.NLNSTTITLT.
RetrocopyPELLHSSSLVKPPAPKTGSIQNNMLTLNLVKQHTGKPESTLETSVNQDTGVGGFHTCFYNLNSTTITLTI
ParentalSNSESIHQSLETQEVLEVTTSHLANPNFTSNSMEIKSAQENPFLFSTINQTVEELNTNKESVIAIFVPAE
SNSESIHQSLETQEVLEVT.S.LANPNFTSNSMEIKSAQENPFLFSTI.QTVEELNTNKESVIAIFVPA.
RetrocopySNSESIHQSLETQEVLEVTSSYLANPNFTSNSMEIKSAQENPFLFSTIKQTVEELNTNKESVIAIFVPAK
ParentalNSKPSVNSFISAQKETTEMEDTDIEDSLYKDVDYGTEVLQIEHSYCRQDINKEHLWQKVSKLHSKITLLE
NSK.SVNSFISAQKETTE.ED.DIEDSLYKDVDYGTEVLQIEHSYCRQDINKEHLWQKVSKLHSKITLLE
RetrocopyNSKLSVNSFISAQKETTEVEDIDIEDSLYKDVDYGTEVLQIEHSYCRQDINKEHLWQKVSKLHSKITLLE
ParentalLKEQQTLGRLKSLEALIRQLKQENWLSEENVKIIENHFTTYEVTMI
.KEQQTLGRLKSLEALIRQLKQENWLSEENVKIIEN.FTTYEVTMI
RetrocopyFKEQQTLGRLKSLEALIRQLKQENWLSEENVKIIENRFTTYEVTMI

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 .20 RPM 28 .56 RPM
bodymap2_adrenal 0 .35 RPM 27 .92 RPM
bodymap2_brain 0 .07 RPM 56 .72 RPM
bodymap2_breast 0 .12 RPM 30 .86 RPM
bodymap2_colon 0 .00 RPM 28 .77 RPM
bodymap2_heart 0 .11 RPM 28 .61 RPM
bodymap2_kidney 0 .10 RPM 45 .72 RPM
bodymap2_liver 0 .04 RPM 24 .91 RPM
bodymap2_lung 0 .00 RPM 33 .00 RPM
bodymap2_lymph_node 0 .24 RPM 37 .79 RPM
bodymap2_ovary 0 .39 RPM 63 .67 RPM
bodymap2_prostate 0 .00 RPM 35 .89 RPM
bodymap2_skeletal_muscle 0 .00 RPM 34 .10 RPM
bodymap2_testis 0 .43 RPM 68 .40 RPM
bodymap2_thyroid 0 .02 RPM 51 .67 RPM
bodymap2_white_blood_cells 0 .10 RPM 57 .70 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3924 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_3924 retrocopy
EST ID Start End Identity Match Mis-match Score
DB297930 158414866 158415406 99.5 540 0 539

TSS - click to see more details

No TSS is located nearby retro_hsap_3924 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3924 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3924 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000032901 retrocopy
retro_cfam_1931,
Homo sapiens ENSG000000419881 retrocopy
retro_hsap_198,
Homo sapiens ENSG00000177683 1 retrocopy
retro_hsap_3924 ,
Myotis lucifugus ENSMLUG000000151301 retrocopy
retro_mluc_1285,
Nomascus leucogenys ENSNLEG000000082901 retrocopy
retro_nleu_2994,

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 = 0.83 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .62 RPM
CEU_NA11843 0 .57 RPM
CEU_NA11930 0 .59 RPM
CEU_NA12004 0 .57 RPM
CEU_NA12400 0 .35 RPM
CEU_NA12751 0 .27 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .80 RPM
CEU_NA12872 0 .19 RPM
CEU_NA12873 0 .61 RPM
FIN_HG00183 0 .63 RPM
FIN_HG00277 0 .30 RPM
FIN_HG00315 0 .69 RPM
FIN_HG00321 0 .36 RPM
FIN_HG00328 0 .50 RPM
FIN_HG00338 0 .28 RPM
FIN_HG00349 0 .43 RPM
FIN_HG00375 0 .20 RPM
FIN_HG00377 0 .25 RPM
FIN_HG00378 0 .40 RPM
GBR_HG00099 0 .46 RPM
GBR_HG00111 0 .37 RPM
GBR_HG00114 0 .50 RPM
GBR_HG00119 0 .29 RPM
GBR_HG00131 0 .29 RPM
GBR_HG00133 0 .46 RPM
GBR_HG00134 0 .48 RPM
GBR_HG00137 0 .38 RPM
GBR_HG00142 0 .83 RPM
GBR_HG00143 0 .29 RPM
TSI_NA20512 0 .37 RPM
TSI_NA20513 0 .80 RPM
TSI_NA20518 0 .19 RPM
TSI_NA20532 0 .68 RPM
TSI_NA20538 0 .51 RPM
TSI_NA20756 0 .20 RPM
TSI_NA20765 0 .58 RPM
TSI_NA20771 0 .37 RPM
TSI_NA20786 0 .10 RPM
TSI_NA20798 0 .28 RPM
YRI_NA18870 0 .37 RPM
YRI_NA18907 0 .28 RPM
YRI_NA18916 0 .34 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .19 RPM
YRI_NA19114 0 .13 RPM
YRI_NA19118 0 .33 RPM
YRI_NA19213 0 .19 RPM
YRI_NA19214 0 .34 RPM
YRI_NA19223 0 .52 RPM

Indel association:

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



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