RetrogeneDB ID:

retro_hsap_1201

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:50464726..50467135(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000181358
Aliases:None
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_1201
ATGGAGGAGCCCGGGGCTACCCCTCAGCCTTACTGGGGGCTGGTCCTGGAGGAGCCACGCAGGGTTGTGGCAGCACTGCC
TGAAGGCAGGAGACCAGATTCGAATCCTTATGGATTTCCATGGGAATTGGTGATATGTGCAGCTGTCCTTGGATTTGTTG
CTGTTCCCTTTTTCTTGTGGAGAAGTTTTAGATCGGTTAGGAGTCGGCTTTATGTGGGAAGAGAGAAAGAGCTTGCTGTA
GCGCTTTCTGGACTAATTGAAGAAAAATGTAGACTACTTGAAAAATTTAGCCTTGTTCAAAAAGAGTATGAAGGCTATGA
AGCAGAGTCACCTTTAGAGGATGCCAGCTTTGAGAAGGAGGCAACAGAAGCACAAAGTTTGGAGGCAAACTGTGAAAAGC
TGAACAGGTCCAATTCTGAACTGGAGCATGAAATACTCTGTCTAGAAAAGGAGTTAAAAGAAGATAAATCTAAACATTCT
GAACAAGATGAGGTGATGGCGGATATTTCCAAAAGGATACAGTCTCTAGAAGATGAGTCAAAATCCCTAAAATCACTGCT
AGCTGAAGCCAAAATGACCTTCAAGAGATTTCAAATGAATGAAGAACAAATGAAGATAGCAATACAAGATGCTTTGAATG
AAAATTCTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAAAGAACAAGTGAGTGAACTTAAT
AAACAGAAAATAACATTTGAAGACTCCAAAGTACACGCAGAACAAGTTCTAAATGATAAAGAAAATCACATCGAGACTCT
GACTGAACGCTTGCTAAAGATCAAAGATCGGGCTGCTATGCTGGAAGAAGACATAACAGATGATGAAAACTTGGAATTAG
AAATGAACAGTGAATCGGAAGATGGTGCTTACTTAGATAATCCTCCAAAAGGAGCTTTGAAGAAACTGATTCATACTGCT
AAGTTAAATGCTTCTTTAACAACCTTAGAAGGAGTAAGAAACCAAATCTATATTCAGTTATCTGAAGTTGATAAAACCAA
GGAAGAGCTTAGAGAGCATATTAAAAATCTTCAGACGGAACAAGCATCTTTGCAGTCAGAAAACACATATTTTGAAAGTG
AGAATCAGAAGCTTCAACAGAAACTTAAGGTAATGACTGAATTATATCAAGAAAATGAAATGAAACTCTACAGGAAATTA
ATAGTAGAGGAAAATAACCGGCTAGAGAAAGAGAAATTTTCTAAAGTAGACGAAATGATCAGCCATGCCACTGAGGAGCT
GGAGACCTACAGAAAGCGAGCCAAATATCTTGAAGAAGAACTTGAGAGAACTATTCATTTTTATCAAGGGAAGATTATAT
ACCATGAGAAAAAAGCACATGATAATTGTTTGGCAGCACAGACCGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAAT
GCTCACAACAGACAAAAATTAATTGAAACAGACTTTAAAATTAAATTTTTAGAAAAAGATCCTTATGCACTTGATGTTCC
AAACACAGCATTTGGCAGAGAGCATTCCTCATATGGTCCCTCACCATTGGGTCGGCCTTCATCTGAAACGAGAGCTTTTC
TCTATCCTCCAACTTTGTCGGAGGGTCCACTCAGACTCTCACCTTTCCCTCCAGGGGGAGGAGGAAGAGGCCCAAGAGGC
CCAGGGAATCCTCTGGACCACCAGATTACCAGTGAAAGAGGAGAATCAAGCTGTAATAGGTTTACTGATCCTCACAAGGC
TCCTTCTGACACTGGGCCCCTGTCACCTCCGTGGGAACAGGACCGTAGGATGATGTTTCCTCCACCAGGACAATCATATC
CTGATTCAGCTCTTCCTCCACAAAGGCAAGACAGATTTTATTCTAATTGTGCTAGACGCTCTGGACCAGCAGAACTCAGA
AGTTTTAATATGCCTTCTTTGGATAAAATGGATGGGTCAGTGCATTCAGAAATGGAATTCAGTGGAAATGATACCAAAGA
TAATCTTGGTAATTTAAATGTGCCTGATTCATCTCTCCCCGCTGAAAGTGAAGCAACTGGCCCTGGCTTTGTTCCTCCAC
CTCTTGCTCCAATCAGAGGTCCGTTGTTTCCAGTGGATACGAGGGGCCCGTTCATGAGAAGAGGACCTCCTTTCCCTCCA
CCTCCTCCAGGAACCATGTTTGGAGCTTCTCCAGATTATTTTCCACCAAGGGATGTCCCAGGTCCACCACGTGCTCCATT
TGCAATGAGAAATGTCTGTCCACTGAGGGGTTTTCCTCCTTACCTTCCCCCAAGACCTGGATTTTCCCCCCCTACCCGCA
CATTCTGAAGGTAGAGTGAGTTCCCTTTAGGGTTGAGTCTGCCTTCAAATGAGCCTGCTGCTGAAGATCCAGAACCATGG
CAAGAAACT

ORF - retro_hsap_1201 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.34 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMEEPGVTPQPYLGLLLEELRRVVAALPEGMRPDSNLYGFPWELVICAAVVGFFAVLFFLWRSFRSVRSRL
MEEPG.TPQPY.GL.LEE.RRVVAALPEG.RPDSN.YGFPWELVICAAV.GF.AV.FFLWRSFRSVRSRL
RetrocopyMEEPGATPQPYWGLVLEEPRRVVAALPEGRRPDSNPYGFPWELVICAAVLGFVAVPFFLWRSFRSVRSRL
ParentalYVGREKKLALMLSGLIEEKSKLLEKFSLVQKEYEGYEVESSLKDASFEKEATEAQSLEATCEKLNRSNSE
YVGREK.LA..LSGLIEEK..LLEKFSLVQKEYEGYE.ES.L.DASFEKEATEAQSLEA.CEKLNRSNSE
RetrocopyYVGREKELAVALSGLIEEKCRLLEKFSLVQKEYEGYEAESPLEDASFEKEATEAQSLEANCEKLNRSNSE
ParentalLEDEILCLEKELKEEKSKHSEQDELMADISKRIQSLEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKD
LE.EILCLEKELKE.KSKHSEQDE.MADISKRIQSLEDESKSLKS..AEAKMTFK.FQMNEE..KIAI.D
RetrocopyLEHEILCLEKELKEDKSKHSEQDEVMADISKRIQSLEDESKSLKSLLAEAKMTFKRFQMNEEQMKIAIQD
ParentalALNENSQLQESQKQLLQEAEVWKEQVSELNKQKVTFEDSKVHAEQVLNDKESHIKTLTERLLKMKDWAAM
ALNENSQLQESQKQLLQEAEVWKEQVSELNKQK.TFEDSKVHAEQVLNDKE.HI.TLTERLLK.KD.AAM
RetrocopyALNENSQLQESQKQLLQEAEVWKEQVSELNKQKITFEDSKVHAEQVLNDKENHIETLTERLLKIKDRAAM
ParentalLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEEL
L.EDITDD.NLELEMNSESE.GAYLDNPPKGALKKLIH.AKLNASL.TLEG.RNQIYIQLSEVDKTKEEL
RetrocopyLEEDITDDENLELEMNSESEDGAYLDNPPKGALKKLIHTAKLNASLTTLEGVRNQIYIQLSEVDKTKEEL
ParentalTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEK
.EHIKNLQTEQASLQSENT.FE.ENQKLQQKLKVMTELYQENEMKL.RKL.VEEN.RLEK.EK.SKVDE.
RetrocopyREHIKNLQTEQASLQSENTYFESENQKLQQKLKVMTELYQENEMKLYRKLIVEENNRLEK-EKFSKVDEM
ParentalISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTE
ISHATEELETYRKRAK.LEEELERTIH.YQG.II.HEKKAHDN.LAA..AERNLNDLRKENAHNRQKL.E
RetrocopyISHATEELETYRKRAKYLEEELERTIHFYQGKIIYHEKKAHDNCLAAQTAERNLNDLRKENAHNRQKLIE
ParentalTELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSR
T..K...LEKDPYALDVPNTAFGREHS.YGPSPLG.PSSETRAFL.PPTL.EGPLRLSP..PGGGGRG.R
RetrocopyTDFKIKFLEKDPYALDVPNTAFGREHSSYGPSPLGRPSSETRAFLYPPTLSEGPLRLSPFPPGGGGRGPR
ParentalGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWDQDRRMMFPPPGQSYPDSALPPQRQDRFCSN
GPGNPLDHQIT.ERGESSC.R.TDPH.APSDTG.LSPPW.QDRRMMFPPPGQSYPDSALPPQRQDRF.SN
RetrocopyGPGNPLDHQITSERGESSCNRFTDPHKAPSDTGPLSPPWEQDRRMMFPPPGQSYPDSALPPQRQDRFYSN
ParentalSGRLSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKDDLGNLNVPDSSLPAENEATGPGFVPPPLAPIR
..R.SGPAELRSFNMPSLDKMDGS..SEME.S.NDTKD.LGNLNVPDSSLPAE.EATGPGFVPPPLAPIR
RetrocopyCARRSGPAELRSFNMPSLDKMDGSVHSEMEFSGNDTKDNLGNLNVPDSSLPAESEATGPGFVPPPLAPIR
ParentalGPLFPVDARGPFLRRGPPFPPPPPGAMFGASRDYFPPGDFPGPPPAPFAMRNVYPPRGFPPYLPPRPGFF
GPLFPVD.RGPF.RRGPPFPPPPPG.MFGAS.DYFPP.D.PGPP.APFAMRNV.P.RGFPPYLPPRPGF.
RetrocopyGPLFPVDTRGPFMRRGPPFPPPPPGTMFGASPDYFPPRDVPGPPRAPFAMRNVCPLRGFPPYLPPRPGFS
ParentalPP-PPHSEGR-SEFPSGLIPPSNEPATEHPEPQQET
PP.P.HSEGR.SEFP.GL..PSNEPA.E.PEP.QET
RetrocopyPP>PAHSEGR<SEFPLGLSLPSNEPAAEDPEPWQET

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 0 .83 RPM
bodymap2_adrenal 0 .02 RPM 1 .68 RPM
bodymap2_brain 0 .00 RPM 0 .96 RPM
bodymap2_breast 0 .00 RPM 1 .09 RPM
bodymap2_colon 0 .00 RPM 0 .66 RPM
bodymap2_heart 0 .00 RPM 0 .63 RPM
bodymap2_kidney 0 .00 RPM 2 .83 RPM
bodymap2_liver 0 .00 RPM 1 .20 RPM
bodymap2_lung 0 .12 RPM 0 .95 RPM
bodymap2_lymph_node 0 .00 RPM 0 .91 RPM
bodymap2_ovary 0 .00 RPM 1 .41 RPM
bodymap2_prostate 0 .00 RPM 1 .11 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .36 RPM
bodymap2_testis 3 .56 RPM 1 .64 RPM
bodymap2_thyroid 0 .00 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_1201 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_1201 retrocopy
EST ID Start End Identity Match Mis-match Score
BI463404 50464651 50465334 96.5 665 8 644

TSS - click to see more details

No TSS is located nearby retro_hsap_1201 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1201 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1201 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_821
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 = 0.03 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 .02 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 .03 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 .03 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 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 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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