RetrogeneDB ID:

retro_hsap_78

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:19995536..19997774(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000212710
Aliases:CTAGE1, CT21.1, CT21.2, CTAGE, CTAGE-1, CTAGE-2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RP11-407N17.3
Ensembl ID:ENSG00000258941
Aliases:CTAGE5, MEA6, MGEA, MGEA11, MGEA6
Description:cTAGE family member 5 isoform 4 [Source:RefSeq peptide;Acc:NP_976231]


Retrocopy-Parental alignment summary:






>retro_hsap_78
ATGAGACCCGATTCTCATCCTTATGGTTTTCCATGGGAATTGGTGATACGTGCAGCTGTTGCTGGATTTTTTGCTGTTCT
CTTCTTGTGGAGAAGTTTTAGATCAGTTACGAGTCGGCTTTATGTGAGAAGAGAGAAAAAGTTTGCTGTGGCACTTTCTG
GACTAATTGAAGAAAAATGTAAACTACTTGAAAAATTTAGCCTTGTTCAAAAAGAGTATGAAGGCTATGAAGTAGAGTCA
TCTTTAAAGAATGCCAGCTTTGAGAAGGAGGCAACAGAAGCACAAAGTTTGGAGGCAACCTGCGAAAAGCTGAACAGGTT
CAATTCTGAACTTGTGCATGAAATACTCTGTCTAGAAAAAGAGTTAAAAGAAGAGAAATCTAAACATTCTGAACAAAATG
AATTGATGGCGGATATTTCCAAAAGGATACAGTCGCTAGAAGATGAGTCAAAATCCCTCAAATCACAAGTAGCTGAAGCC
AAAATGACCTTCAAGAGATTTCAAGCGAATGAAGAACGGTTGGAGATAGAAATACAAGATGCTTGGAAAGAAAATTCTGA
ACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAAAGAACAAGTGAGTGAACTTATTAAACAGAAAA
GAACATTTGAAGACTCCAAAGTACATGCAGAACAAGTTCTAAATGATAAAGAAAATCACATCAAGACTCTGACTGAACGC
TTGCTAAAGATGAAAGATGGGGTTGCTATGCTTGAAGAAGATGTAACGGATGATGATAACTTGGAATTAGAAATGAACAG
TGAATCGGAAGATGGTGCTTACTTAGATAATCCTCCAAAAGGAGCTTTGAAGAAACTGATTCATGCTGCTAAGTTAAATG
CTTCCTTAAAAACCTTAGAAGGAGAAAGAAACCAAATTTATATTCAATTATCTGAAGTTGATAAAACAAAGGAAGAGCTT
ACAGAGCATATTAAAAATCTTCAGACTGAACAAGCATCTTTGCAGTCAGAAAACACACATTTTGAAAGTGAGAATCAGAA
GCTTCAGCAGAAACTTAAAGTAATGACTGAATTATATCAAGAAAATGAAATGAAACTCTACAGGAAATTAATAGTAGAGG
AAAAATGCCGGTTAGAGAAAGAAGAGAAACTTTCTAAAGTAGACGAAATGATCAGCCATGCCACTGAAGAGCTGGAGACC
TACCGAAAGCGAGCCAAAGATCTTAAAGAATTTGAGAAAACTATTCATTTTTATCAAAAGAAGATTATTCTCCATGAGAA
AAAAGCACATGATAATTGGTCGGCAGCTTGGACTGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAATGCTCACAACA
GACAAAAATTAACTGAAATAGAGTTTAAAATAAAACTTTTAGAAAAAGATCCTTATGGACTTGATGTTCCAAATACAGCA
TTTGGCAGACAGCATTCCCCATATGGTCCCTCACCATTGGGTTGGCCTTCATCTGAAACGAGAGCTTCTCTCTATCCTCC
AACTTTGTTGGAAGGTCCTCTCAGACTCTCACCTTTGCTTCCACGGGGAGGAGGAAGAGGCTCCAGAGGCCCAGGGAATC
CTCCGGACCATCAGATTACCAAAGAAAGAGGAGAATCAAGCTGTGATAGGTTAACTGATCCTCACAGGGCTCCTTCTGAC
GCTGGGCCCCTGGCACCTCCGTGGGAACAGGACTATAGGATGATGTTTCCTCCACCAGGACAATCATATCCTGATTCAGC
TCTCCCTCCACAAAGGCAAGACAGATTTTATTCTAATTGTGCTAGACTCTCTGGACCAGCAGAACTCAGAAGTTTTAATA
TGCCTTCTTTGGATAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCCAGTAGAAATGATACCAAAGATAATCTTGGT
AATTTAAAGGTGCCTGATTCATCTCTCCCCGCTGAAAATGAAGCAACTGGCCCTGGCTTTGTTCCTCCACCTCTTGCTCC
AATCAGAGGTTTATTGTTTCCAGTAGATACAAGGGGCCCGTTCATAAGAAGAGGACCTCCTTTCCCCCCACCTCCTCCAG
GAACCGTGTTTGGAGCTTCTCCAGATTATTTTTCTCCAAGGGATGTCCCAGGTCCACCACGTGCTCCATTTGCAATGAGA
AATGTCTATTTACCGAGAGGTTTTCTTCCTTACCGTCCCCCAAGACCTGCATTTTTCCCCCCAGCCCCCACATTCTGA

ORF - retro_hsap_78 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.59 %
Parental protein coverage: 55.64 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMRPDSNLYGFPWELVICAAVVGFFAVLFFLWRSFRSVRSRLYVGREKKLALMLSGLIEEKSKLLEKFSLV
MRPDS..YGFPWELVI.AAV.GFFAVLF.LWRSFRSV.SRLYV.REKK.A..LSGLIEEK.KLLEKFSLV
RetrocopyMRPDSHPYGFPWELVIRAAVAGFFAVLF-LWRSFRSVTSRLYVRREKKFAVALSGLIEEKCKLLEKFSLV
ParentalQKEYEGYEVESSLKDASFEKEATEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHSEQDELMADI
QKEYEGYEVESSLK.ASFEKEATEAQSLEATCEKLNR.NSEL..EILCLEKELKEEKSKHSEQ.ELMADI
RetrocopyQKEYEGYEVESSLKNASFEKEATEAQSLEATCEKLNRFNSELVHEILCLEKELKEEKSKHSEQNELMADI
ParentalSKRIQSLEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALNENSQLQESQKQLLQEAEVWKEQVSEL
SKRIQSLEDESKSLKSQVAEAKMTFK.FQ.NEERL.I.I.DA..ENS.LQESQKQLLQEAEVWKEQVSEL
RetrocopySKRIQSLEDESKSLKSQVAEAKMTFKRFQANEERLEIEIQDAWKENSELQESQKQLLQEAEVWKEQVSEL
ParentalNKQKVTFEDSKVHAEQVLNDKESHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPP
.KQK.TFEDSKVHAEQVLNDKE.HIKTLTERLLKMKD..AML.ED.TDDDNLELEMNSESE.GAYLDNPP
RetrocopyIKQKRTFEDSKVHAEQVLNDKENHIKTLTERLLKMKDGVAMLEEDVTDDDNLELEMNSESEDGAYLDNPP
ParentalKGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFENENQKLQ
KGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFE.ENQKLQ
RetrocopyKGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFESENQKLQ
ParentalQKLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSY
QKLKVMTELYQENEMKL.RKL.VEE..RLEKEEKLSKVDE.ISHATEELETYRKRAKDL..E.E.TIH.Y
RetrocopyQKLKVMTELYQENEMKLYRKLIVEEKCRLEKEEKLSKVDEMISHATEELETYRKRAKDL-KEFEKTIHFY
ParentalQGQIISHEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPY
Q..II.HEKKAHDNW.AA..AERNLNDLRKENAHNRQKLTE.E.K..LLEKDPY.LDVPNTAFGR.HSPY
RetrocopyQKKIILHEKKAHDNWSAAWTAERNLNDLRKENAHNRQKLTEIEFKIKLLEKDPYGLDVPNTAFGRQHSPY
ParentalGPSPLGWPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCDRLTDPHRAP
GPSPLGWPSSETRA.L.PPTLLEGPLRLSPLLP.GGGRGSRGPGNP.DHQIT.ERGESSCDRLTDPHRAP
RetrocopyGPSPLGWPSSETRASLYPPTLLEGPLRLSPLLPRGGGRGSRGPGNPPDHQITKERGESSCDRLTDPHRAP
ParentalSDTGSLSPPWDQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEM
SD.G.L.PPW.QD.RMMFPPPGQSYPDSALPPQRQDRF.SN..RLSGPAELRSFNMPSLDKMDGSMPSEM
RetrocopySDAGPLAPPWEQDYRMMFPPPGQSYPDSALPPQRQDRFYSNCARLSGPAELRSFNMPSLDKMDGSMPSEM
ParentalESSRNDTKDDLGNLNVPDSSLPAENEATGPGFVPPPLAPIRGPLFPVDARGPFLRRGPPFPPPPPGAMFG
ESSRNDTKD.LGNL.VPDSSLPAENEATGPGFVPPPLAPIRG.LFPVD.RGPF.RRGPPFPPPPPG..FG
RetrocopyESSRNDTKDNLGNLKVPDSSLPAENEATGPGFVPPPLAPIRGLLFPVDTRGPFIRRGPPFPPPPPGTVFG
ParentalASRDYFPPGDFPGPPPAPFAMRNVYPPRGFPPYLPPRPGFFPPPP
AS.DYF.P.D.PGPP.APFAMRNVY.PRGF.PY.PPRP.FFPP.P
RetrocopyASPDYFSPRDVPGPPRAPFAMRNVYLPRGFLPYRPPRPAFFPPAP

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 .00 RPM
bodymap2_adrenal 0 .00 RPM 0 .00 RPM
bodymap2_brain 0 .00 RPM 0 .00 RPM
bodymap2_breast 0 .00 RPM 0 .00 RPM
bodymap2_colon 0 .00 RPM 0 .00 RPM
bodymap2_heart 0 .00 RPM 0 .00 RPM
bodymap2_kidney 0 .00 RPM 0 .56 RPM
bodymap2_liver 0 .00 RPM 0 .30 RPM
bodymap2_lung 0 .00 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 0 .00 RPM
bodymap2_ovary 0 .04 RPM 0 .00 RPM
bodymap2_prostate 0 .00 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 6 .49 RPM 0 .00 RPM
bodymap2_thyroid 0 .00 RPM 0 .00 RPM
bodymap2_white_blood_cells 0 .02 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_78 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_78 retrocopy
EST ID Start End Identity Match Mis-match Score
AA398146 19995608 19995848 99.6 239 1 238

TSS - click to see more details

No TSS is located nearby retro_hsap_78 retrocopy 5' end.

Lab - click to see more details

retro_hsap_78 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_78 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1286
Pongo abelii retro_pabe_1588
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 ENSG000001505273 retrocopies
retro_hsap_1201, retro_hsap_3691, retro_hsap_640,
Homo sapiens ENSG00000258941 1 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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .04 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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