RetrogeneDB ID:

retro_hsap_3670

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:138026565..138028338(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000220412
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_3670
AGACAATGGTTTCACCCAAATATCAGTGGTGTGGAGGCAGAAAAACCTATTGTCGACAAGAGGAGTTGATGGCAGTTTTT
TGGCAAGGCCTAGTAAAAGTACCCCTGGAGACTTCACATGTTCCATTAGAAGAAATAGAGCTGTCACCCACATCAAGATT
CAGAACACTGGTGATTACTAGGACCCGTTTGGGGGGAAAAGTTTGCCACTTCGGCTGAGTTGGTCCAGTATTACATGGAA
CATCACAGGCAATTAAAAGAGAAGAATGGAGATGTTGTTGAGCTTAAATATCCTCTGAACTGTGCGGATCCTGCCTCTGA
AAGATGGTTTCACGGACACCTCTTTGGGAAAGAAGCAGAGAAATTAACTGAAAAAGGAAAACATGGTAGCTTTCTTATAC
GAGAGAGCCAGAGCCACCCTGGAGATTTTGTTCTCTCTGTGCGCACCAGTGATGACAAAAAAGAGAGCAATGACAGCAAG
TGTAAAGTGACCCATGTCATGATTCGCTGTCAGGAACTGAAATACGACGTTGGTGGAGGAAAACGGTTTGATTCTTTGAC
GGATCTCGTGGAACATTACAAGAAGAATCCTATGCTGGAAACATTGGGTACAGTACTACGACTCAAGCAGCCCCTTAACA
TGACTCGTATAAATGCTGCTGAAATAGAAAGCAGAGTTTGAGAACTAAGCAAATTAGCTGAGACCACAGACAAAGTCCAA
CAAGGCTTTTGGGAAGAATTTGAGACACTACAACCACAGGAGTGCAAACTTCTCTACAGCCGAAAAGAGGGTCAAAGGCA
AGAAAACAAAAACAAAAATAGATATAAAAACATCCTGCCCTTTGATCATACCAGGGTTGTCCTACACGATGATGATCCCA
ATGAGCCTATTTCAGATTACATCAGTGCAAACACCATCATGCCTGAATTTGAAACCAAGTGCAACAATTCAAAACCCAAA
AAGAGTTGCATTGCCACACAAGGCTGCCTGCAAAACATGGTGAATGACTTTTGCTGGATGGTGTTCCAAGAAAACTCCCA
AGTGATTGTCATGACAATGAAAGAAATGGAGAGAGGAAAGAGTAAATGTGTCAAATACTGGTCTGAAGAGGATGCTCTAC
AAGAATATGGGGTCATGTGTGTTAGGAACATCAAAGGAAGTGCTGTTCATGACTATATGCTAAGAGAACTTAAGTTTTCA
AAGGTTGGACAAGCTGTACTCCAGGGGAATATGGCGAGAACGGTCTGGCAATACCACTTTCGGACCTGACCAGACCACGG
AGTGCCCAGTGACCCCGGGGGCATGCTGGACTTCCTGGAGGAGGTGCACCATAAGCAGGAGAGCATCATGGATGCAGGGC
TGGTCGTGGTCCACTGCAGTGCTGGAATTGGCCATACAGGGAGGTTCATTGTGATTAATAGTCTTATTGACATCATCAGA
GAGAAAGGTATTAACTGCAACATTGACCTTCTCAAAACCATCCACACAGTGCAGTCTCAGAGGTCAGGGATGGCCCAGAC
AGAAGCACAGTACCGATTTATCTATATGGCAGTCCAGCATTATATTGAAACACTACAGCACAAGATTGAAGAAGAGCAGA
AAAGCAAGAGGAAAGGGCACGAATATAAAAATATTAAGTATTCTCTAGCAGACCAGACAAGTGGAGCCCAGAGCCCCCTC
CCGCCTTGCACTGCAGCGCCACCCTGTGCAGAAATGAGAGAAGACAATGCTGGAGTCTGTGAAAACGTGGACCTGATACA
ACAGAAAAGTTTC

ORF - retro_hsap_3670 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.87 %
Parental protein coverage: 99.33 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalRRWFHPNITGVEAE-NLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGG-EKF
R.WFHPNI.GVEAE.NLL.TRGVDGSFLARPSKS.PGDFT.S.RRN.AVTHIKIQNTGDY.D..GG.EKF
RetrocopyRQWFHPNISGVEAE>NLLSTRGVDGSFLARPSKSTPGDFTCSIRRNRAVTHIKIQNTGDY*DPFGG<EKF
ParentalATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQ
AT.AELVQYYMEHH.QLKEKNGDV.ELKYPLNCADP.SERWFHGHL.GKEAEKL.TEKGKHGSFL.RESQ
RetrocopyATSAELVQYYMEHHRQLKEKNGDVVELKYPLNCADPASERWFHGHLFGKEAEKL-TEKGKHGSFLIRESQ
ParentalSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQ
SHPGDFVLSVRT.DDK.ESND.K.KVTHVMIRCQELKYDVGGG.RFDSLTDLVEHYKKNPM.ETLGTVL.
RetrocopySHPGDFVLSVRTSDDKKESNDSKCKVTHVMIRCQELKYDVGGGKRFDSLTDLVEHYKKNPMLETLGTVLR
ParentalLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKN
LKQPLN.TRINAAEIESRV.ELSKLAETTDKV.QGFWEEFETLQ.QECKLLYSRKEGQRQ..........
RetrocopyLKQPLNMTRINAAEIESRV*ELSKLAETTDKVQQGFWEEFETLQPQECKLLYSRKEGQRQXXXXXXXXXX
ParentalILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSR
.LPFDHTRVVLHD.DPNEP.SDYI.AN.IMPEFETKCNNSKPKKS.IATQGCLQN.VNDF..MVFQENS.
RetrocopyXLPFDHTRVVLHDDDPNEPISDYISANTIMPEFETKCNNSKPKKSCIATQGCLQNMVNDFCWMVFQENSQ
ParentalVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQ----GNTERTVWQ
VIVMT.KE.ERGKSKCVKYW..E.AL.EYGVM.VRN.K.SA.HDY.LRELK.SKVGQ....GN..RTVWQ
RetrocopyVIVMTMKEMERGKSKCVKYWSEEDALQEYGVMCVRNIKGSAVHDYMLRELKFSKVGQAVLQGNMARTVWQ
ParentalYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCD
YHFRT.PDHGVPSDPGG.LDFLEEVHHKQESIMDAG.VVVHCSAGIG.TG.FIVI..LIDIIREKG..C.
RetrocopyYHFRT*PDHGVPSDPGGMLDFLEEVHHKQESIMDAGLVVVHCSAGIGHTGRFIVINSLIDIIREKGINCN
ParentalIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKYSLADQTSGDQ
ID..KTI..V.SQRSGM.QTEAQYRFIYMAVQHYIETLQ..IEEEQKSKRKGHEY.NIKYSLADQTSG.Q
RetrocopyIDLLKTIHTVQSQRSGMAQTEAQYRFIYMAVQHYIETLQHKIEEEQKSKRKGHEYKNIKYSLADQTSGAQ
ParentalSPLPPCTPTPPCAEMREDSARVYENVGLMQQQKSF
SPLPPCT..PPCAEMRED.A.V.ENV.L..QQKSF
RetrocopySPLPPCTAAPPCAEMREDNAGVCENVDLI-QQKSF

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 .25 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 .12 RPM 155 .10 RPM
bodymap2_lymph_node 0 .00 RPM 127 .17 RPM
bodymap2_ovary 0 .08 RPM 141 .82 RPM
bodymap2_prostate 0 .00 RPM 171 .56 RPM
bodymap2_skeletal_muscle 0 .02 RPM 276 .40 RPM
bodymap2_testis 0 .79 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_3670 was not detected

EST - click to see more details

2 EST(s) were mapped to retro_hsap_3670 retrocopy
EST ID Start End Identity Match Mis-match Score
AW393812 138026652 138026964 99.1 309 3 306
BU658061 138026840 138027337 99 492 5 487

TSS - click to see more details

No TSS is located nearby retro_hsap_3670 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3670 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3670 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_1792
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 = 0.39 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .09 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .23 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .08 RPM
CEU_NA12873 0 .13 RPM
FIN_HG00183 0 .16 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .39 RPM
FIN_HG00328 0 .21 RPM
FIN_HG00338 0 .11 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .13 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .14 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .22 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .17 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .12 RPM
YRI_NA19213 0 .12 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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





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