RetrogeneDB ID:

retro_hsap_4899

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:128175518..128177160(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000234592
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TJAP1
Ensembl ID:ENSG00000137221
Aliases:TJAP1, PILT, TJP4
Description:tight junction associated protein 1 (peripheral) [Source:HGNC Symbol;Acc:17949]


Retrocopy-Parental alignment summary:






>retro_hsap_4899
ATAACCAGTGCAGCCCCTGCTAAGAAACCCTACCGTAAGGCACCACCAGAGCATTGGGAGCTGCGACTGGAAATTCCTGG
ATCCAGGTTTGAGCAGGAGGAATCCCTGACTGACTTGGAAAGGATGAAGCTCTCGCAGCAGGATAATGAAGAGCTTTGTC
GGTGCCTGGCCTCGGCCACGAGATGCACTGAGGTCCTGGAATGTAAGCTGGAAATTGGGCAGGACTGCCTAGAGCTGGAG
CTGCGCCAGAGCCGCAAGGAGCTGGACAAGTTTTAAGGATAAGTTCTGCAGGCTGCAGAACAGCTACATGGCTTCCCAGC
AGACCAACCAGGAGTTGGAGGACAAGCTGCACACACTGCTCAAGAAGGCTGAGATGGATAGGCAGACGCTGGACTGGGAG
ATCGTGGAGCTGACCAACAAGCTGCTGGATGCCAAGAACACCATCAACAAGCTGGAGGAGCTCAGCGAGCGGTACCAGGG
GGATTGCAACCTGGCTGTGCAGCTCCTCAAGTGCAGCCAGTCCCACTTCCGAAACTATGAGTTCTCCGATCTGTCCTGTG
AGCTACACGACATGGTTCAGAAACATCTGCATAGTGGACAAGAGGCCGCCAGCCCGGGTCCTGCTCCCAGCCTAGCCCCA
GCGGCTGTTGTGCCTACTTTGGTCATTGCCCGAGTGTTAGAGAAGCCAGAGTCTCTACTGCTGAATTCAGCCCGGTCAGG
CAGCGCTGGGCACCCTATGGCTGAAGATGTCTTTGTGCATGTGGACATCAGTGAGGGTGCCCCAGGCGATCCAGCCAGTC
CCCCGGCCCCTGGCAGCCCCACCCCCCAACCCAATGGGGAGTGTCACTCTCTGGATACTGCTGGGGGCTCCCCAGAGGAA
GAGCTGCCCCTGCCAGCCTTTGAGAAGCTGAGCCCCTACCCCACCCCATCTCCACCACTCCCACTGTATCCTGGCTGCAG
GGTAATAGAGTTCTCCAAGGATAAAGTTTGGATCCCCTGCAACAGCCCCCTGCCCAACTGCACTTACACCACCCGCCAGG
CCATTTCGCTGAGCCTGGTGGGGGAAGGGAGTGAGTGGGCCTGCCCCAGCCCAGTGCTCAGTGCCCCTGCCTCAGCCTAG
GCCTCACTCAACCACCAGCCCAGCTCAGTGCTCCCAACACTCAGTGCCCCAGCCAGGTCTGTTAGCTCTGAAAAGGACCT
GCTGGTCAGCTGGCAGTGGGCATTTGTGGACCATACTCTGCCACCTGCTGCTGTGGCCCAGGTCACAGCCTTTAAGAGTG
ACACCCTCCCTGAGCTGCAGCACCGTTTTGCCCATAACTCCGCTGACAGAGATTAGGTGGTCCAGGCACCTTCTCCCCGA
ACCAAAGAGAGTGGGCTTTTGCTTCCCACAGAACCTGACTCTGGCTTTCCCAGGGAGGAGGAAGAAGAGCTGAACCTGCC
CATCCGCCCTGAGGAAGAGCGCCAGAGCCTGCTGCTCATTAACAGTGTCACAGAGGAGGGTCCTGGCACTTCCCACACTG
AGCGCAGGGCCTGGCCACTCCCCAGCTCCAGCCACCCCCAGTGCAGCCCCAAAAGAATGGGGGTTCACCACCTGCACTGC
AAGGACAGCCTGACGCAGGCCCAGCAGCAGGGCAACCAGCTC

ORF - retro_hsap_4899 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.11 %
Parental protein coverage: 99.82 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMTSAAPAKKPYRKAPPEHRELRLEIPGSRLEQEEPLTDAERMKLLQEENEELRRRLASATRRTEALEREL
.TSAAPAKKPYRKAPPEH.ELRLEIPGSR.EQEE.LTD.ERMKL.Q..NEEL.R.LASATR.TE.LE..L
RetrocopyITSAAPAKKPYRKAPPEHWELRLEIPGSRFEQEESLTDLERMKLSQQDNEELCRCLASATRCTEVLECKL
ParentalEIGQDCLELELGQSREELDKF-KDKFRRLQNSYTASQRTNQELEDKLHTLIKKAEMDRKTLDWEIVELTN
EIGQDCLELEL.QSR.ELDKF.KDKF.RLQNSY.ASQ.TNQELEDKLHTL.KKAEMDR.TLDWEIVELTN
RetrocopyEIGQDCLELELRQSRKELDKF>KDKFCRLQNSYMASQQTNQELEDKLHTLLKKAEMDRQTLDWEIVELTN
ParentalKLLDAKNTINKLEELNERYRLDCNLAVQLLKCNKSHFRNHKFADLPCELQDMVRKHLHSGQEAASPGPAP
KLLDAKNTINKLEEL.ERY..DCNLAVQLLKC..SHFRN..F.DL.CEL.DMV.KHLHSGQEAASPGPAP
RetrocopyKLLDAKNTINKLEELSERYQGDCNLAVQLLKCSQSHFRNYEFSDLSCELHDMVQKHLHSGQEAASPGPAP
ParentalSLAPGAVVPTSVIARVLEKPESLLLNSAQSGSAGRPLAEDVFVHVDMSEGVPGDPASPPAPGSPTPQPNG
SLAP.AVVPT.VIARVLEKPESLLLNSA.SGSAG.P.AEDVFVHVD.SEG...................G
RetrocopySLAPAAVVPTLVIARVLEKPESLLLNSARSGSAGHPMAEDVFVHVDISEGXXXXXXXXXXXXXXXXXXXG
ParentalECHSLGTARGSPEEELPLPAFEKLNPYPTPSPPHPLYPGRRVIEFSEDKVRIPRNSPLPNCTYATRQAIS
ECHSL.TA.GSPEEELPLPAFEKL.PYPTPSPP.PLYPG.RVIEFS.DKV.IP.NSPLPNCTY.TRQAIS
RetrocopyECHSLDTAGGSPEEELPLPAFEKLSPYPTPSPPLPLYPGCRVIEFSKDKVWIPCNSPLPNCTYTTRQAIS
ParentalLSLVEEGSERARPSPVPSTPASAQASPHHQPSPAPLTLSAPASSASSEEDLLVSWQRAFVDRTPPPAAVA
LSLV.EGSE.A.PSPV.S.PASA.AS..HQPS....TLSAPA.S.SSE.DLLVSWQ.AFVD.T.PPAAVA
RetrocopyLSLVGEGSEWACPSPVLSAPASA*ASLNHQPSSVLPTLSAPARSVSSEKDLLVSWQWAFVDHTLPPAAVA
ParentalQRTAFGRDALPELQRHFAHSPADRDEVVQAPSARPEESELLLPTEPDSGFPR-EEEELNLPISPEEERQS
Q.TAF..D.LPELQ..FAH..ADRD.VVQAPS.R..ES.LLLPTEPDSGFPR.EEEELNLPI.PEEERQS
RetrocopyQVTAFKSDTLPELQHRFAHNSADRD*VVQAPSPRTKESGLLLPTEPDSGFPREEEEELNLPIRPEEERQS
ParentalLLPINRGTEEGPGTSHTEGRAWPLPSSSRPQRSPKRMGVHHLHRKDSLTQAQEQGNLL
LL.IN..TEEGPGTSHTE.RAWPLPSSS.PQ.SPKRMGVHHLH.KDSLTQAQ.QGN.L
RetrocopyLLLINSVTEEGPGTSHTERRAWPLPSSSHPQCSPKRMGVHHLHCKDSLTQAQQQGNQL

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 14 .93 RPM
bodymap2_adrenal 0 .00 RPM 27 .86 RPM
bodymap2_brain 0 .00 RPM 18 .61 RPM
bodymap2_breast 0 .00 RPM 15 .56 RPM
bodymap2_colon 0 .00 RPM 11 .50 RPM
bodymap2_heart 0 .02 RPM 8 .88 RPM
bodymap2_kidney 0 .00 RPM 15 .35 RPM
bodymap2_liver 0 .00 RPM 6 .65 RPM
bodymap2_lung 0 .00 RPM 14 .98 RPM
bodymap2_lymph_node 0 .00 RPM 26 .46 RPM
bodymap2_ovary 0 .00 RPM 25 .54 RPM
bodymap2_prostate 0 .00 RPM 27 .16 RPM
bodymap2_skeletal_muscle 0 .00 RPM 35 .68 RPM
bodymap2_testis 0 .00 RPM 18 .63 RPM
bodymap2_thyroid 0 .00 RPM 22 .39 RPM
bodymap2_white_blood_cells 0 .00 RPM 16 .03 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4899 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4899 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4899 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4899 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4899 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3267
Gorilla gorilla retro_ggor_3059
Pongo abelii retro_pabe_3811
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000137221 1 retrocopy
retro_hsap_4899 ,
Gorilla gorilla ENSGGOG000000151851 retrocopy
retro_ggor_3059,
Pongo abelii ENSPPYG000000166421 retrocopy
retro_pabe_3811,
Pan troglodytes ENSPTRG000000181991 retrocopy
retro_ptro_3267,

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 ) Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 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 .00 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 .00 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 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



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