RetrogeneDB ID:

retro_pabe_3593

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:Un:41604789..41606614(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DLGAP4
Ensembl ID:ENSPPYG00000010970
Aliases:None
Description:disks large-associated protein 4 [Source:RefSeq peptide;Acc:NP_001127321]


Retrocopy-Parental alignment summary:






>retro_pabe_3593
ATGAAAGGCCTCAGTGACAGCCGCCCCCACCACCTCTCTAGGGACAGCCTAGACCCACCCCACGAGCCCGATTGCAGGGA
CCGACCACAACTCCTACCTGCTGTCGCCCACGGAGGCCTTCGCTGGCAAGGCCCGCTTCCCTGGGCAGGACACCCTGCTG
GGGGATGGCCCCTTTCCCCACAACAACCTGCTGCCCCCGCCCAGCAGCACCTTTCCCTGCATCCACGACAACTCCCACTT
CGAGGTGCCAGAGGAGATCCCCTTCCCCAGCCATGCCCAGGCCACCAAGATCAACCGGCTGCCCACCAACCTACTGGTCC
AGTTTGAGAAGCAGCTGCCCGTCCACCGTGGTGGCTTCAGCACCCTCCAATTCCCCCGTGGTGAGACCAAGGCCCATGGC
GAGAGCCCTGGCCGCATCCACCACCTGGTCCACTCAGTCCAGCGGCTTTTCTTCACCAAGGCACCCTCACTGGATGGCAC
AGTGGGCAAGGTCGGTGGCAATGGCAGCAAGAAGGGTGGCATTGAGGACTGGCAAGGGCCAGAGGGCCAAAAGCAAGGAG
CGGGCCAAGGTTGGGGAGCCCAAAGGGTGCAGCTGCTCCAACATCTCAGGCTGGTGGAGCGCCGATGACAACTTGGATGG
CGAGGCCAGCACCTTCCGCAGCAGTGGCCCAGCCTCCGGGCTGATGACACTAGGCTGCCAGGCAGAACGCAGCCAGCCAC
GCTACTTCATGCACGCCTACAACACCCTCAGTGGGCACATGCTCAAAACCACCAAGAAAACACCACCTAGCTGACCGTCC
CACCACCCCCTCCTGCACCCCAAGCCACCTGCCCCAGCCTTGGGGTGGGCACTGACACCAACTACGTCAAACGGGGCTCC
TGGTTCACTCTGACCCTCAGCCACACCCACGAAGTCTGCCAGAAGACCTCGGCCACCTTTGATAAGAGCGTGCTCAAGCC
CAAATCCTGCCACCAGGGTCCAGCCTACCATTACCCGCAGGTGCCTGGCGGTGGCGAGTGCAGCACCACGATGCTGTCCC
CACGTGAGATGGATGCCACAGCCGACGGCCCCAGCCCATTCCGGCTCATGCGCAGCAGCAGCTACATCAAGGCCATGGGC
AACAAGGACAGCGACGAGTCCGGCCGCAGCTCCGAGCCCTCACCCAAGACTGCAGCGCGGCGCCAGAGCTATCTGCGGGT
CACGCAGCCATCACTGGGAGAGCAGAGCAACCCCCACAGGAGTCTGGACTGCCTGGAGTCAGTGGACATGCTGCTGCCCT
CCAAGTGTCCGGGCTGGGAAGAGGACTACATGCCCATCAGTGACAGCCTCAACGACTCCAGCTGCATCAGCCAGATTTTT
GGACAGGCCTCCCTGATCCCCCAGTTGTTTGGCCATGAGCAGCAGGTACAGGAGGCAGAGCCGAGTGAACAGGATGAGGC
GGCCTGCAAGTCAGCCTGCAGTGAAGCGGAGTCCACAGTGGCAGAAATGCTTGATTTGCCACTGCCTAGCTGCTTCCGCT
CCCGCAGCCCCAGCTACCTGCGTGCCATCCAGGCAGGCTGCTTGCAGGAGGAGGACAGTGTCTCCCTGCAGTCCCTCTCC
CCACCACCCGGTACCAGCAGCCTCAGCAATAGTCGCAGCCTTCCGAGTTCATCATGCCTAGTGGCGTATAAGAAGACCCT
GCCACCGGTCCCTCCATGCACCACTTCAAAGCCGTTCATCTCAGTCACAGTCCAGAGCGGTACTGAGTCTGCCCAGGATA
CCTACCTGGATAGCCAGGACCACAAGAGCGAGGTGACTAGCCAGTTGGGTCTGAGCAACCCATCA

ORF - retro_pabe_3593 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.67 %
Parental protein coverage: 61.39 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMKGLGDSRPRHLS-DSLDPPHE-PLFAGTDRNPYLLSPTEAFAREARFPGQNTLPGDGLFPLNNQLPPPS
MKGL.DSRP.HLS.DSLDPPHE.P..AGTD.N.YLLSPTEAFA..ARFPGQ.TL.GDG.FP.NN.LPPPS
RetrocopyMKGLSDSRPHHLSRDSLDPPHE>PI-AGTDHNSYLLSPTEAFAGKARFPGQDTLLGDGPFPHNNLLPPPS
ParentalSTFPRIHYNSHFEVPEESPFPSHAQATKINRLPANLLDQFEKQLPIHRDGFSTLQFPRGEAKARGESPGR
STFP.IH.NSHFEVPEE.PFPSHAQATKINRLP.NLL.QFEKQLP.HR.GFSTLQFPRGE.KA.GESPGR
RetrocopySTFPCIHDNSHFEVPEEIPFPSHAQATKINRLPTNLLVQFEKQLPVHRGGFSTLQFPRGETKAHGESPGR
ParentalIRHLVHSVQRLFFTKAPSLEGTAGKVGGNGSKKGGIEE-GKGRSAKSKERAKAGEPKRRSRSNISGWWSS
I.HLVHSVQRLFFTKAPSL.GT.GKVGGNGSKKGGIE..GKG..AKSKERAK.GEPK..S.SNISGWWS.
RetrocopyIHHLVHSVQRLFFTKAPSLDGTVGKVGGNGSKKGGIED>GKGQRAKSKERAKVGEPKGCSCSNISGWWSA
ParentalDDNLDGEAGAFRSSGPASGLMTLGRQAERSQPRYFMHAYNTISGHMLKATKN-NTTELTAPPPPPAPPAT
DDNLDGEA..FRSSGPASGLMTLG.QAERSQPRYFMHAYNT.SGHMLK.TK..NTT.LT.PPPPPAP.AT
RetrocopyDDNLDGEASTFRSSGPASGLMTLGCQAERSQPRYFMHAYNTLSGHMLKTTKK<NTT*LTVPPPPPAPQAT
ParentalCPSLGVGTDTNYVKRGSWSTLTLSHAHEVCQKTSATLDKSLLKSKSCHQGLAYHYLQVPGGGGEWSTTLL
CPSLGVGTDTNYVKRGSW.TLTLSH.HEVCQKTSAT.DKS.LK.KSCHQG.AYHY.QVPGGG.E.STT.L
RetrocopyCPSLGVGTDTNYVKRGSWFTLTLSHTHEVCQKTSATFDKSVLKPKSCHQGPAYHYPQVPGGG-ECSTTML
ParentalSPRETDAAAEGPIPCRRMRSGSYIKAMGDEDSDESGGSPKPSPKTAARRQSYLRATQQSLGEQSNPRRSL
SPRE.DA.A.GP.P.R.MRS.SYIKAMG..DSDESG.S..PSPKTAARRQSYLR.TQ.SLGEQSNP.RSL
RetrocopySPREMDATADGPSPFRLMRSSSYIKAMGNKDSDESGRSSEPSPKTAARRQSYLRVTQPSLGEQSNPHRSL
ParentalDRLDSVDMLLPSKCPSWEEDYTPVSDSLNDSSCISQIFGQASLIPQLFGHEQQVREAELSDQYEAACESA
D.L.SVDMLLPSKCP.WEEDY.P.SDSLNDSSCISQIFGQASLIPQLFGHEQQV.EAE.S.Q.EAAC.SA
RetrocopyDCLESVDMLLPSKCPGWEEDYMPISDSLNDSSCISQIFGQASLIPQLFGHEQQVQEAEPSEQDEAACKSA
ParentalCSEAESTAAETLDLPLPSYFRSRSHSYLRAIQAGCSQEEDSVSLQSLSPPPSTGSLSNSRTLPSSSCLVA
CSEAEST.AE.LDLPLPS.FRSRS.SYLRAIQAGC.QEEDSVSLQSLSPPP.T.SLSNSR.LPSSSCLVA
RetrocopyCSEAESTVAEMLDLPLPSCFRSRSPSYLRAIQAGCLQEEDSVSLQSLSPPPGTSSLSNSRSLPSSSCLVA
ParentalYKKTPPPVPPRTTSKPFISVTVQSSTESAQDTYLDSQDHKSEVTSQSGLSNSS
YKKT.PPVPP.TTSKPFISVTVQS.TESAQDTYLDSQDHKSEVTSQ.GLSN.S
RetrocopyYKKTLPPVPPCTTSKPFISVTVQSGTESAQDTYLDSQDHKSEVTSQLGLSNPS

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
SRP007412_brain_prefrontal_cortex 0 .00 RPM 74 .31 RPM
SRP007412_cerebellum 0 .00 RPM 16 .05 RPM
SRP007412_heart 0 .00 RPM 5 .75 RPM
SRP007412_kidney 0 .00 RPM 16 .77 RPM
SRP007412_liver 0 .00 RPM 4 .90 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_3593 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3593 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3593 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Pongo abelii ENSPPYG00000010970 2 retrocopies
retro_pabe_3555, retro_pabe_3593 ,


Copyright © RetrogeneDB 2014-2017