RetrogeneDB ID:

retro_hsap_640

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:131904309..131906715(+)
Located in intron of:ENSG00000237489
Retrocopy
information
Ensembl ID:ENSG00000233122
Aliases:CTAGE7P, CTAGE7, CTAGEP, bA500G10.2, rcCTAGE5
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CTAGE5
Ensembl ID:ENSG00000150527
Aliases:None
Description:CTAGE family, member 5 [Source:HGNC Symbol;Acc:7057]


Retrocopy-Parental alignment summary:






>retro_hsap_640
ATGTTGGAGCCAGGGGCTACCCCTCAGCGGTACTTGGGGCTGGTCCTGGGGGAGCCACGCAGGGTTGTGGCAGCGCTGCC
TGAAAGTATGAGACTGGATTCGAATCCTCATGGTTTTCCATGGGAAATGGTGATATGTGCAGCTGTTGCTGCATTTTTTG
CTGTTCTCCTTTTTCTGTGGAGAAGTTTTAGATCGGTTAGGAGTCGGCTTTATGTGGGAAGAGAGAAAAAGCTTGCTATA
ATGCTTTCTGGACTAATTGAAGAAAAATGTAAACTACTTGAAAAATTTAGCCTTGTTCAAAAAGAGTATGAAGACTATGA
AGTAGCGTCATCGTTAGAGGATGCCAGCTTTGAGAAGGCGGCAGCAGAAGCACGAAGTTTGGAGGCAACCTGTGAAAAGT
TGAACAGGTCCAATTCTGAACTTGAGCATGAAATTCTCTGTCTAGAAAAAGAGTTAAAAGAAGAGAAATCTAAACATTCG
CAACAAAATGAATTGATGGCGGATATTTCAAAAACGATACAGCCTCTAGCAGATGAGTCAGAATCCCTCAAATCACAAGT
AGCTGAAGCCAAAATGATCTTCAAGAGATTTAAAATGACTGAGAAACAACTGAAGATAGCAATAAAAGATGCTTTGAATG
AAAACTCTCACCTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAACGAACAAGTGAATGAACTTAAT
AAACAGAAAATAACATTTGAAGACTCCAAAGTACATGCAGAACAAGTTCTAAATGATAAAGAAAATCACATCAAGACTCT
GACTGAACATTTGCTAAAGATGAAAGATTGGGCTGCTAGGCTTAGAGAAGACGTAACGGATGATGATAACTTAGAAGTGA
ACAGTGAATCAGAAGATGGTGCTTACTTAGATGATCCTCTAAAAGGAGCTCTGAAGAAACTGATTCATGCTACTAAGTTA
AATGCTTCTTTAAAAACCTTAGAAGGAGAAAGAAACCAAATTTATATCCAGTTACCTGAAATTGATAAAACAAAGGAAGA
GCTTACAGAGCATATTAAAAATCTTCGGACTGAACAAGCATCTTTGCAGTCAGAAAACACACATTTTGAAAGTGAGAATC
AGAAGCTTCAACAGAAACTTAAAGTAATGACTGAATTATATCAAGAAAATGAAATGAAACTCTACAGGAAATTAACAGTA
GAGGAAAATAGCCGGTTAGAGAAAGAAGAGAAACTTTCTAAGGTAGACAAAAAGATCAGCCATGCCACTAAAGAGCTGGA
GACCTACAGACAGCGAGCCAAAGATCTTGAAGAAGAATTGGAGAGAACTATTCATTATTATCAACGGCAGATTATTTCCC
ATGAGAAAAAGGCACATCATAACTGGTTGGCAGCTTGGGCTGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAATGCT
CACAACAGACAAAAATTAGCTGAAACAGAGTATAAAATAAAACTTCTAAAAAAAGATCCTTATGTACTTGATGTTCCAAA
TACAGCATTTGGCAGAGAGCATTCCCCATATGGTCCCTCATCATTGGGTCGGCCTTCATCTGAAACGAGAGCTTTTCTCT
CTCCCGCAACTCTGTTGGAGGGTCCACTCAGACTCTCACCTTTGCCTCCAGGGGGGGAAGGAAGAGGCTCAAGAGGCCCA
GGGAATCCTCTGGACCATCAGATTACCAAGGAAAGAGGAGAATCAAGCTGTGAAAGGTTAACCGATCCTCACAGGTCTCC
TTCTGACACTGGGTCCCTGTCACTTCCGAGGGAACAGGACCGTAGGATGATGTTTCCTCCACCAGCGCAATCATATCTTG
ATTCAGCTCTTCCTCCACAAAGGCAAGACAGATTTTATTCTAACTCTGGTGGACTGTCTGGACCAGCAGAACTCAGAAGT
TTTAATATGCCTCCTTTGGATAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCCAGTAGAAATGACACCAAAGATGA
TCTTGGTAATTTAAATATCCCTGATTCATCTCTCCCTGCTGAAAATGCAGCAACTGGCCCTCGCTTTGTTCCTCCACCTC
TTGCCCTAATCAGAGGTCCACTGTTTCCAGTGGATACAAGGGGCCCGTTCATGAGAAGAGCACCTCCTTTCCCCCCACCT
CCTCCAGGAACCAGGTTTGGAGCTTCTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCACATGCTCCGTTTGC
AATGAGAAATGTCTATCCACCGAGGGGTTTTCCTCCTTACCCTCCCCCAAGACCTGGATTTTTCCCCCGACCCCCACATT
CTGAAGGTAGAAGTGAGTTCCCTTCAGGGCTGATTCCGCCTTCAAATGAGCCTGCTACGGAACATCCAAAACCGCAGCAA
GATACC

ORF - retro_hsap_640 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.44 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEEPGVTPQPYLGLLLEELRRVVAALPEGMRPDSNLYGFPWELVICAAVVGFFAVLFFLWRSFRSVRSRL
M.EPG.TPQ.YLGL.L.E.RRVVAALPE.MR.DSN..GFPWE.VICAAV..FFAVL.FLWRSFRSVRSRL
RetrocopyMLEPGATPQRYLGLVLGEPRRVVAALPESMRLDSNPHGFPWEMVICAAVAAFFAVLLFLWRSFRSVRSRL
ParentalYVGREKKLALMLSGLIEEKSKLLEKFSLVQKEYEGYEVESSLKDASFEKEATEAQSLEATCEKLNRSNSE
YVGREKKLA.MLSGLIEEK.KLLEKFSLVQKEYE.YEV.SSL.DASFEK.A.EA.SLEATCEKLNRSNSE
RetrocopyYVGREKKLAIMLSGLIEEKCKLLEKFSLVQKEYEDYEVASSLEDASFEKAAAEARSLEATCEKLNRSNSE
ParentalLEDEILCLEKELKEEKSKHSEQDELMADISKRIQSLEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKD
LE.EILCLEKELKEEKSKHS.Q.ELMADISK.IQ.L.DES.SLKSQVAEAKM.FK.F.M.E..LKIAIKD
RetrocopyLEHEILCLEKELKEEKSKHSQQNELMADISKTIQPLADESESLKSQVAEAKMIFKRFKMTEKQLKIAIKD
ParentalALNENSQLQESQKQLLQEAEVWKEQVSELNKQKVTFEDSKVHAEQVLNDKESHIKTLTERLLKMKDWAAM
ALNENS.LQESQKQLLQEAEVW.EQV.ELNKQK.TFEDSKVHAEQVLNDKE.HIKTLTE.LLKMKDWAA.
RetrocopyALNENSHLQESQKQLLQEAEVWNEQVNELNKQKITFEDSKVHAEQVLNDKENHIKTLTEHLLKMKDWAAR
ParentalLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEEL
L.ED.TDDDNLE...NSESE.GAYLD.P.KGALKKLIHA.KLNASLKTLEGERNQIYIQL.E.DKTKEEL
RetrocopyLREDVTDDDNLEV--NSESEDGAYLDDPLKGALKKLIHATKLNASLKTLEGERNQIYIQLPEIDKTKEEL
ParentalTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEK
TEHIKNL.TEQASLQSENTHFE.ENQKLQQKLKVMTELYQENEMKL.RKLTVEEN.RLEKEEKLSKVD.K
RetrocopyTEHIKNLRTEQASLQSENTHFESENQKLQQKLKVMTELYQENEMKLYRKLTVEENSRLEKEEKLSKVDKK
ParentalISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTE
ISHAT.ELETYR.RAKDLEEELERTIH.YQ.QIISHEKKAH.NWLAA..AERNLNDLRKENAHNRQKL.E
RetrocopyISHATKELETYRQRAKDLEEELERTIHYYQRQIISHEKKAHHNWLAAWAAERNLNDLRKENAHNRQKLAE
ParentalTELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSR
TE.K..LL.KDPY.LDVPNTAFGREHSPYGPS.LG.PSSETRAFLSP.TLLEGPLRLSPL.PGG.GRGSR
RetrocopyTEYKIKLLKKDPYVLDVPNTAFGREHSPYGPSSLGRPSSETRAFLSPATLLEGPLRLSPLPPGGEGRGSR
ParentalGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWDQDRRMMFPPPGQSYPDSALPPQRQDRFCSN
GPGNPLDHQIT.ERGESSC.RLTDPHR.PSDTGSLS.P..QDRRMMFPPP.QSY.DSALPPQRQDRF.SN
RetrocopyGPGNPLDHQITKERGESSCERLTDPHRSPSDTGSLSLPREQDRRMMFPPPAQSYLDSALPPQRQDRFYSN
ParentalSGRLSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKDDLGNLNVPDSSLPAENEATGPGFVPPPLAPIR
SG.LSGPAELRSFNMP.LDKMDGSMPSEMESSRNDTKDDLGNLN.PDSSLPAEN.ATGP.FVPPPLA.IR
RetrocopySGGLSGPAELRSFNMPPLDKMDGSMPSEMESSRNDTKDDLGNLNIPDSSLPAENAATGPRFVPPPLALIR
ParentalGPLFPVDARGPFLRRGPPFPPPPPGAMFGASRDYFPPGDFPGPPPAPFAMRNVYPPRGFPPYLPPRPGFF
GPLFPVD.RGPF.RR.PPFPPPPPG..FGASRDYFPPGDFPGPP.APFAMRNVYPPRGFPPY.PPRPGFF
RetrocopyGPLFPVDTRGPFMRRAPPFPPPPPGTRFGASRDYFPPGDFPGPPHAPFAMRNVYPPRGFPPYPPPRPGFF
ParentalPPPPHSEGRSEFPSGLIPPSNEPATEHPEPQQET
P.PPHSEGRSEFPSGLIPPSNEPATEHP.PQQ.T
RetrocopyPRPPHSEGRSEFPSGLIPPSNEPATEHPKPQQDT

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 .04 RPM 0 .83 RPM
bodymap2_adrenal 0 .27 RPM 1 .68 RPM
bodymap2_brain 0 .28 RPM 0 .96 RPM
bodymap2_breast 0 .14 RPM 1 .09 RPM
bodymap2_colon 0 .17 RPM 0 .66 RPM
bodymap2_heart 0 .04 RPM 0 .63 RPM
bodymap2_kidney 0 .74 RPM 2 .83 RPM
bodymap2_liver 0 .00 RPM 1 .20 RPM
bodymap2_lung 0 .23 RPM 0 .95 RPM
bodymap2_lymph_node 1 .50 RPM 0 .91 RPM
bodymap2_ovary 0 .52 RPM 1 .41 RPM
bodymap2_prostate 0 .74 RPM 1 .11 RPM
bodymap2_skeletal_muscle 0 .05 RPM 0 .36 RPM
bodymap2_testis 2 .39 RPM 1 .64 RPM
bodymap2_thyroid 0 .09 RPM 2 .88 RPM
bodymap2_white_blood_cells 0 .00 RPM 1 .56 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_640 was not detected

EST - click to see more details

4 EST(s) were mapped to retro_hsap_640 retrocopy
EST ID Start End Identity Match Mis-match Score
BI461938 131904272 131904853 99.9 578 1 575
CV023017 131904309 131904985 99.6 666 2 658
DA027794 131904382 131904932 100 550 0 550
DB272697 131904535 131905092 100 557 0 557

TSS - click to see more details

No TSS is located nearby retro_hsap_640 retrocopy 5' end.

Lab - click to see more details

retro_hsap_640 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_640 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_466
Pongo abelii retro_pabe_29
Parental genes homology:
Parental genes homology involve 9 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000161054 retrocopies
retro_cjac_1747, retro_cjac_2711, retro_cjac_3217, retro_cjac_921,
Cavia porcellus ENSCPOG000000265142 retrocopies
retro_cpor_189, retro_cpor_727,
Homo sapiens ENSG00000150527 3 retrocopies
retro_hsap_1201, retro_hsap_3691, retro_hsap_640 ,
Homo sapiens ENSG000002589411 retrocopy
retro_hsap_78,
Gorilla gorilla ENSGGOG000000119901 retrocopy
retro_ggor_936,
Nomascus leucogenys ENSNLEG0000000412110 retrocopies
retro_nleu_1218, retro_nleu_1690, retro_nleu_2087, retro_nleu_2103, retro_nleu_2148, retro_nleu_2600, retro_nleu_2951, retro_nleu_3017, retro_nleu_3077, retro_nleu_688,
Pongo abelii ENSPPYG000000057689 retrocopies
retro_pabe_1001, retro_pabe_1002, retro_pabe_1007, retro_pabe_1055, retro_pabe_1060, retro_pabe_1588, retro_pabe_2119, retro_pabe_29, retro_pabe_3024,
Pan troglodytes ENSPTRG0000000629710 retrocopies
retro_ptro_1286, retro_ptro_1712, retro_ptro_2503, retro_ptro_2580, retro_ptro_2880, retro_ptro_466, retro_ptro_821, retro_ptro_826, retro_ptro_868, retro_ptro_876,
Ictidomys tridecemlineatus ENSSTOG000000158901 retrocopy
retro_itri_95,

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 = 1.11 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .28 RPM
CEU_NA11843 0 .40 RPM
CEU_NA11930 0 .78 RPM
CEU_NA12004 0 .34 RPM
CEU_NA12400 0 .60 RPM
CEU_NA12751 0 .97 RPM
CEU_NA12760 0 .58 RPM
CEU_NA12827 0 .61 RPM
CEU_NA12872 0 .57 RPM
CEU_NA12873 0 .89 RPM
FIN_HG00183 0 .80 RPM
FIN_HG00277 0 .96 RPM
FIN_HG00315 0 .50 RPM
FIN_HG00321 0 .70 RPM
FIN_HG00328 0 .38 RPM
FIN_HG00338 0 .19 RPM
FIN_HG00349 0 .37 RPM
FIN_HG00375 0 .49 RPM
FIN_HG00377 0 .15 RPM
FIN_HG00378 0 .21 RPM
GBR_HG00099 0 .52 RPM
GBR_HG00111 0 .37 RPM
GBR_HG00114 0 .32 RPM
GBR_HG00119 0 .55 RPM
GBR_HG00131 0 .57 RPM
GBR_HG00133 0 .27 RPM
GBR_HG00134 0 .68 RPM
GBR_HG00137 0 .30 RPM
GBR_HG00142 0 .78 RPM
GBR_HG00143 0 .26 RPM
TSI_NA20512 0 .17 RPM
TSI_NA20513 1 .11 RPM
TSI_NA20518 0 .56 RPM
TSI_NA20532 0 .34 RPM
TSI_NA20538 0 .74 RPM
TSI_NA20756 0 .23 RPM
TSI_NA20765 0 .50 RPM
TSI_NA20771 0 .34 RPM
TSI_NA20786 0 .26 RPM
TSI_NA20798 0 .28 RPM
YRI_NA18870 0 .85 RPM
YRI_NA18907 0 .55 RPM
YRI_NA18916 0 .67 RPM
YRI_NA19093 0 .21 RPM
YRI_NA19099 0 .56 RPM
YRI_NA19114 0 .34 RPM
YRI_NA19118 0 .66 RPM
YRI_NA19213 0 .55 RPM
YRI_NA19214 0 .34 RPM
YRI_NA19223 1 .09 RPM

Indel association:

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



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