RetrogeneDB ID:

retro_hsap_3302

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:23303713..23304928(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000250332
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PTPN11
Ensembl ID:ENSG00000179295
Aliases:PTPN11, BPTP3, CFC, NS1, PTP-1D, PTP2C, SH-PTP2, SH-PTP3, SHP2
Description:protein tyrosine phosphatase, non-receptor type 11 [Source:HGNC Symbol;Acc:9644]


Retrocopy-Parental alignment summary:






>retro_hsap_3302
AAGGAACTGAAATATGACGTTGGTGGAGGAGAACGGTTTGATTCTTTAACAGATCTTGAAGAACATTACAAGAAGAATTC
CATGGTGGAAACCTTGGGTACAGTACTACAACTCAAGCATCCCCTTAACACGACTCATATAAATGCTGCTGAAATAAAAA
GCAGAGTTCGAGAACTAAGCAAATTAGCTGAGACCACAGACAAACTCAAACAAGGCTTTTGGGAAAAATTTGAGACACTA
CAACAACAGGAGTGCAAACTTCTCTACAGCCGAAAAGAGGGTCAAAGGCAAGAAAACAAAAACAAAAATAGATATAAAAA
CATCCTACCCTTTGATCATACTAGGGTTGTCCTACACGACGGTGATCCCGATGAGCCTGTTTCAGATTACATCAGTGCAA
ATACCATCATGCCTGAATTTGAAACCAGGTGCAACAATTCAAAGCCCAAAACGTGTTACATTGCCACACAAGGCTGTCAG
CAAAACACAGTGAATGACTTTTGGCAGATGAAGTTCCAAGAAAACTCCCGAGTGATTGTCATGACAACAAAAGAAGTGGA
TAGAGGAAAGAGTAAATGTGTCAAATACTGGCCTGATGAGTATGCTTTAAAAGAATATGGCGTCATGCGTGTTAGGAACG
TCAAAGAAAGCGCAGCTCATGACTATACACTAAGAGAACTTGAACTTTCAAAGATTGGACCAGGGAATATGGAGAGACCG
GTCGGGCAATATCACTTTCGGACCTGGCCGGACCATGGAGTGCCCAGCGACCCCGGGGTCGTGCTGGACTTCCTGGAGGA
GGTGTACCATAAGCAGGGGAGCATCACGGATGCAGGGCCGGTCGTGGTGCACTGTAGTGCTGGAATTGGCCTGACAGGGA
CGTTCATTGTGATTGATATTCTTACTGACATCGTCAGAGAGAAAGGTGTTGACTGCAACATTGACGTTCCCAAAACCATC
CAGATGATGCGGTCTCAGAGGTCAGGGATGGTCCAGACAGAAGCATAGTACCGATTTATCTATACGGCAGTCCAGCATTA
TATTGAAACACTGCAGCTCAGGATTGAAGAAGAGCAAAAAAGCAAGAGGAAAGGGCACGAATATATAAATATTAAGTATT
CTCTAGCGGACCAGAAGAGTGGAGATCAGAGCCCCCTCCTGCCTTGTACTCCAACGCCACCCTGTGCAGAAATGAGAGAA
GACAGTGCTAGAGTC

ORF - retro_hsap_3302 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.93 %
Parental protein coverage: 68.3 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVK
.ELKYDVGGGERFDSLTDL.EHYKKN.MVETLGTVLQLK.PLNTT.INAAEI.SRVRELSKLAETTDK.K
RetrocopyKELKYDVGGGERFDSLTDLEEHYKKNSMVETLGTVLQLKHPLNTTHINAAEIKSRVRELSKLAETTDKLK
ParentalQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEF
QGFWE.FETLQQQECKLLYS..................LPFDHTRVVLHDGDP.EPVSDYI.AN.IMPEF
RetrocopyQGFWEKFETLQQQECKLLYSXXXXXXXXXXXXXXXXXXLPFDHTRVVLHDGDPDEPVSDYISANTIMPEF
ParentalETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMR
ET.CNNSKPK..YIATQGC.QNTVNDFW.M.FQENSRVIVMTTKEV.RGKSKCVKYWPDEYALKEYGVMR
RetrocopyETRCNNSKPKTCYIATQGCQQNTVNDFWQMKFQENSRVIVMTTKEVDRGKSKCVKYWPDEYALKEYGVMR
ParentalVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGP
VRNVKESAAHDYTLREL.LSK.G.GN.ER.V.QYHFRTWPDHGVPSDPG.VLDFLEEV.HKQ.SI.DAGP
RetrocopyVRNVKESAAHDYTLRELELSKIGPGNMERPVGQYHFRTWPDHGVPSDPGVVLDFLEEVYHKQGSITDAGP
ParentalVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIET
VVVHCSAGIG.TGTFIVIDIL.DI.REKGVDC.IDVPKTIQM.RSQRSGMVQTEA.YRFIY.AVQHYIET
RetrocopyVVVHCSAGIGLTGTFIVIDILTDIVREKGVDCNIDVPKTIQMMRSQRSGMVQTEA*YRFIYTAVQHYIET
ParentalLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQSPLPPCTPTPPCAEMREDSARV
LQ.RIEEEQKSKRKGHEY.NIKYSLADQ.SGDQSPL.PCTPTPPCAEMREDSARV
RetrocopyLQLRIEEEQKSKRKGHEYINIKYSLADQKSGDQSPLLPCTPTPPCAEMREDSARV

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 263 .94 RPM
bodymap2_adrenal 0 .00 RPM 132 .33 RPM
bodymap2_brain 0 .00 RPM 394 .29 RPM
bodymap2_breast 0 .00 RPM 407 .53 RPM
bodymap2_colon 0 .00 RPM 244 .85 RPM
bodymap2_heart 0 .00 RPM 230 .25 RPM
bodymap2_kidney 0 .00 RPM 164 .18 RPM
bodymap2_liver 0 .00 RPM 136 .31 RPM
bodymap2_lung 0 .00 RPM 155 .10 RPM
bodymap2_lymph_node 0 .00 RPM 127 .17 RPM
bodymap2_ovary 0 .00 RPM 141 .82 RPM
bodymap2_prostate 0 .00 RPM 171 .56 RPM
bodymap2_skeletal_muscle 0 .00 RPM 276 .40 RPM
bodymap2_testis 0 .00 RPM 163 .74 RPM
bodymap2_thyroid 0 .00 RPM 231 .81 RPM
bodymap2_white_blood_cells 0 .00 RPM 123 .01 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3302 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3302 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3302 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3302 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3302 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 7 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000124641 retrocopy
retro_cjac_1051,
Homo sapiens ENSG000001753542 retrocopies
retro_hsap_1186, retro_hsap_480,
Homo sapiens ENSG00000179295 5 retrocopies
retro_hsap_2823, retro_hsap_3061, retro_hsap_3302 , retro_hsap_3670, retro_hsap_4062,
Gorilla gorilla ENSGGOG000000106891 retrocopy
retro_ggor_1962,
Macaca mulatta ENSMMUG000000132534 retrocopies
retro_mmul_1501, retro_mmul_1792, retro_mmul_1877, retro_mmul_2345,
Nomascus leucogenys ENSNLEG000000000785 retrocopies
retro_nleu_1200, retro_nleu_1360, retro_nleu_1654, retro_nleu_522, retro_nleu_561,
Pongo abelii ENSPPYG000000049764 retrocopies
retro_pabe_2205, retro_pabe_2535, retro_pabe_2825, retro_pabe_3336,

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 = 0.04 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 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 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 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

The presence of retro_hsap_3302 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_3302 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. 5:23303355..23304800 100 98.86 100 100 100 100 100 100 100 100 100 100 100 100

Indel #1, located at the genomic coordinates 5:23303355..23304800.

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 98.86 % 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 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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