RetrogeneDB ID:

retro_hsap_2745

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:195723713..195724485(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000231464
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PPP4R2
Ensembl ID:ENSG00000163605
Aliases:PPP4R2, PP4R2
Description:protein phosphatase 4, regulatory subunit 2 [Source:HGNC Symbol;Acc:18296]


Retrocopy-Parental alignment summary:






>retro_hsap_2745
GAGAAACAGATTCCGTGGTCCCAATTTAAAGGCTATTTTATTTTCAAACTGGAGAAAGTGATGGATGATTTCAGAACTTC
AGCTCCTGTGCCAAGAGGTCCTCCCAACCCTAATGTCGAATATATTCCCTTTGATGCAACAAAGGGAAGAATACTGAAAA
CTGTCACTGGATTTAACCGTATCCCTTTTACTATTCAGCGACTATTGAATTGTTAACAGATCCAAGGAGAAACTATACAG
GAACAGACAAATTTCTCAGAGGAGTAGAAAAGAACGTGATGGTTGTTAGCTGTGTTTATCCTTCTTCAGAGAAAAACAAT
TCCAATAGTTTAAATCGAATGAATGGTGTGATGTTTCCTGGAAATGCACCAAGCTATACTGAGAGGTCTAATATAAATGG
GCCTGGGACACCCAGGCCACGTAATCGACCAAAGGTTTCTCTGTCAGCCCCCATGACAACAAATGGGTGGCCTGATAGCA
CAGACAGCAAAGAGGCAAATTTGCAGCAAAATGAAGAGAAAACTCACAGTGACTCTTCGACATCTGAATCAGAAGTTTCC
TCAGTGAGCCCTTTGAGAAATAAACATCCAGATGAAGATGCTGTGGAAGCTGAGGGGCATGAGGTAAAAAGACTCAGGTT
TGACAAAAAGGCGAAGTCGGAGAAATAGCCAGTCAAGCGACTTGCAGCGAAATTTCTTCAGTTGTGGTAGAAGAAACAGA
AGCATCACCTTCATCCCATGATAAAGACAAAGAAAGCCGTGGTACCCGGCAG

ORF - retro_hsap_2745 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.85 %
Parental protein coverage: 61.87 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalETMIQWSQFKGYFIFKLEKVMDDFRTSAPEPRGPPNPNVEYIPFDEMKERILKIVTGFNGIPFTIQRLC-
E..I.WSQFKGYFIFKLEKVMDDFRTSAP.PRGPPNPNVEYIPFD..K.RILK.VTGFN.IPFTIQRL..
RetrocopyEKQIPWSQFKGYFIFKLEKVMDDFRTSAPVPRGPPNPNVEYIPFDATKGRILKTVTGFNRIPFTIQRLL<
ParentalELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYPSSEKNNSNSLNRMNGVMFPGNSPSYTERSNINGPGTPR
ELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYPSSEKNNSNSLNRMNGVMFPGN.PSYTERSNINGPGTPR
RetrocopyELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYPSSEKNNSNSLNRMNGVMFPGNAPSYTERSNINGPGTPR
ParentalPLNRPKVSLSAPMTTNGLPESTDSKEANLQQNEEKNHSDSSTSESEVSSVSPLKNKHPDEDAVEAEGHEV
P.NRPKVSLSAPMTTNG.P.STDSKEANLQQNEEK.HSDSSTSESEVSSVSPL.NKHPDEDAVEAEGHEV
RetrocopyPRNRPKVSLSAPMTTNGWPDSTDSKEANLQQNEEKTHSDSSTSESEVSSVSPLRNKHPDEDAVEAEGHEV
ParentalKRLRFDK-EGEVRETASQTTSSEISSVMVGETEASSSSQDKDKDSRCTRQ
KRLRFDK..GEV.E.ASQ.T.SEISSV.V.ETEAS.SS.DKDK.SR.TRQ
RetrocopyKRLRFDK<KGEVGEIASQATCSEISSVVVEETEASPSSHDKDKESRGTRQ

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 76 .99 RPM
bodymap2_adrenal 0 .00 RPM 72 .67 RPM
bodymap2_brain 0 .07 RPM 89 .21 RPM
bodymap2_breast 0 .00 RPM 90 .37 RPM
bodymap2_colon 0 .00 RPM 91 .05 RPM
bodymap2_heart 0 .00 RPM 95 .06 RPM
bodymap2_kidney 0 .12 RPM 88 .84 RPM
bodymap2_liver 0 .00 RPM 52 .75 RPM
bodymap2_lung 0 .09 RPM 110 .44 RPM
bodymap2_lymph_node 0 .00 RPM 92 .03 RPM
bodymap2_ovary 0 .02 RPM 128 .06 RPM
bodymap2_prostate 0 .00 RPM 67 .93 RPM
bodymap2_skeletal_muscle 0 .04 RPM 78 .92 RPM
bodymap2_testis 0 .08 RPM 122 .17 RPM
bodymap2_thyroid 0 .00 RPM 88 .32 RPM
bodymap2_white_blood_cells 0 .00 RPM 100 .59 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2745 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2745 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2745 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2745 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2745 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000079543 retrocopies
retro_chof_1347, retro_chof_1914, retro_chof_2285,
Echinops telfairi ENSETEG000000199462 retrocopies
retro_etel_1238, retro_etel_148,
Homo sapiens ENSG00000163605 6 retrocopies
retro_hsap_2744, retro_hsap_2745 , retro_hsap_2746, retro_hsap_2904, retro_hsap_3138, retro_hsap_3283,
Loxodonta africana ENSLAFG000000005131 retrocopy
retro_lafr_603,
Macaca mulatta ENSMMUG000000169591 retrocopy
retro_mmul_1224,
Mus musculus ENSMUSG000000521443 retrocopies
retro_mmus_1068, retro_mmus_1157, retro_mmus_3474,
Oryctolagus cuniculus ENSOCUG000000062351 retrocopy
retro_ocun_292,
Pan troglodytes ENSPTRG000000151085 retrocopies
retro_ptro_1855, retro_ptro_1856, retro_ptro_2121, retro_ptro_2220, retro_ptro_2974,

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 = 0.24 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 0 .20 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .21 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .24 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .22 RPM
GBR_HG00137 0 .16 RPM
GBR_HG00142 0 .17 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .10 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .10 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .10 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM

Indel association:

The presence of retro_hsap_2745 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_2745 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 3:195669672..195729000 100 100 100 100 100 100 100 100 100 98.92 100 100 99.48 99.5

Indel #1, located at the genomic coordinates 3:195669672..195729000.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 98.92 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 99.48 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 99.5 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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