RetrogeneDB ID:

retro_pabe_3555

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:Un:65635888..65637713(+)
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_3555
ATGAAAGGCCTCGGTGACAGCCGCCCCCACCACCTCTCTAGGGACAGCCTAGACCCACCCCACGAGCCCGTTTGCAGGGA
CCGACCGCAACTCCTACCTGCTGTCGCCCACGGAGGCCTTCGCCGGCAAGGCCCGCTTCCCTGGGCAGGACACCCTGCCG
GGGGATGGCCTCTTTCCCCACAACAACCAGCTGCCCCCGCCCAGCAGCACCTTTCCCTGCATCCACGACAACTCCCACTT
CGAGGTGCCAGAGGAGAGCCCCTTCCCCAGCCATGCCCAGGCCACCAAGATCAACCGGCTGCCCACCAACCTCCTGGTCC
AGTTTGAGAAGCAGCTGCCCGTCCACCGTGGTGGCTTCAGCACCCTCCAGTTCCCCCGTGGTGAGACCAAGGCCCGTGGC
GAGAGCCCTGGCCGCATCCGCCACCTGGTCCACTCAGTCCAGCGGCTTTTCTTCACCAAGGCACCCTCACTGGATGGCAC
AGTGGGCAAGGTCGGTGGCAATGGCAGCAAGAAGGGTGGCATGGAGGACTGGCAAGGGCCAGAGGGCCAAAAGCAAGGAG
CGGGCCAAGGTTGGGGAGCCCAAAGGGCGCAGCCGCTCCAACATCTCAGGCTGGTGGAGCGCCGATGACAACTTGGATGG
CGAGGCCGGCACCTTCCGCAGCAGTGGCCCAGCCTCCGGGCTGATGACACTAGGCCGCCAGGCAGAACGCAGCCAGCCAC
GCTACTTCATGCACGCCTACAACACCCTCAGTGGGCACATGCTCAAAGCCACCAAGAACACACCACCCAGCTGACCGCCC
CACCACCTCCGCCTGCACCCCCAGCCACCTGCCCCAGCCTTGGGGTGGGCACTGACACCAACTACGTCAAACGGGGCTCC
TGGTCCACTCTGACCATCAGCCACGCCCACGAGGTCTGCCAGAAGACCTCGGCCACCTTTGATAAGAGCGTGCTCAAGCC
CAAATCCTGCCACCAGGGTCTAGCCTACCATTACCCGCAGGTGCCTGGCGGCGGCGAGTGCAGCACAACGATGCTGTCCC
CACGCGAGACAGATGCCGCAGCCAAGGGCCCCAGCCCGTTCCGGCTCATGCGCAGCAGCAGCTACATCAAGGCCATGGGC
GACAAGGACAGCGACGAGTCCGGCCGCAGCCCCGAGCCCTCACCCAAGACCGCAGCGCGGCGCCAGAGCTATCTGAAGGT
CACGCAGCCGTCACTGGGAGAGCAGAGCAACCCCCACAGGAGTCTGGACCGCCTGGATTCAGTGGACATGCTGCTGCCCT
CCAAGTGTCCGGGCTGGGAAGAGGACTACATGCCCGTCAGTGACAGCCTCAACGACTCCAGCTGCATCAGCCAGATTTTT
GGACAGGCCTCCCTGATCCCCTAGTTGTTTGGCCACGAGCAGCAGGTACGGGAGGCAGAGCCCAGTGAACCGGATGAGGC
GGCCTGCGAGTCAGCCTGCAGTGAAGCGGAGTCCACAGCGGCGGAGATGCTTGATTTGCCACTGCCCAGCTGCTTCCGCT
CCCGCAGCCCCAGCTACCTGCGTGCCATCCAGGCAGGCTGCTCGCAGGAAGAGGACAGTGTCTCCCTGCAGTCCCTCTCC
CCACCACCCGGTACCAGCAGCCTCAGCAATAGTTGCAGCCTTCCGAGTTCATCATGCCTAGTGGCGTATAAGAAGACCCT
GCCACCAGTCCCTCCATGCACCACTTCAAAGCCGTTCATCTCAGTCACAGTCCAGAGCGGTACTGAGTCTGCCCAGGATA
CCTACCTGGACAGCCAGGACCACAAGAGCGAGGTGACTAGCCAGTTGGGCCTGAGCAACTCATCA

ORF - retro_pabe_3555 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.42 %
Parental protein coverage: 61.39 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMKGLGDSRPRHLS-DSLDP-PHEPLFAGTDRNPYLLSPTEAFAREARFPGQNTLPGDGLFPLNNQLPPPS
MKGLGDSRP.HLS.DSLDP.P..P.FAGTDRN.YLLSPTEAFA..ARFPGQ.TLPGDGLFP.NNQLPPPS
RetrocopyMKGLGDSRPHHLSRDSLDP>PTSP-FAGTDRNSYLLSPTEAFAGKARFPGQDTLPGDGLFPHNNQLPPPS
ParentalSTFPRIHYNSHFEVPEESPFPSHAQATKINRLPANLLDQFEKQLPIHRDGFSTLQFPRGEAKARGESPGR
STFP.IH.NSHFEVPEESPFPSHAQATKINRLP.NLL.QFEKQLP.HR.GFSTLQFPRGE.KARGESPGR
RetrocopySTFPCIHDNSHFEVPEESPFPSHAQATKINRLPTNLLVQFEKQLPVHRGGFSTLQFPRGETKARGESPGR
ParentalIRHLVHSVQRLFFTKAPSLEGTAGKVGGNGSKKGGIEE-GKGRSAKSKERAKAGEPKRRSRSNISGWWSS
IRHLVHSVQRLFFTKAPSL.GT.GKVGGNGSKKGG.E..GKG..AKSKERAK.GEPK.RSRSNISGWWS.
RetrocopyIRHLVHSVQRLFFTKAPSLDGTVGKVGGNGSKKGGMED>GKGQRAKSKERAKVGEPKGRSRSNISGWWSA
ParentalDDNLDGEAGAFRSSGPASGLMTLGRQAERSQPRYFMHAYNTISGHMLKATKN-NTTELTAPPPPPAPPAT
DDNLDGEAG.FRSSGPASGLMTLGRQAERSQPRYFMHAYNT.SGHMLKATKN..TT.LTAPPPPPAPPAT
RetrocopyDDNLDGEAGTFRSSGPASGLMTLGRQAERSQPRYFMHAYNTLSGHMLKATKN<HTTQLTAPPPPPAPPAT
ParentalCPSLGVGTDTNYVKRGSWSTLTLSHAHEVCQKTSATLDKSLLKSKSCHQGLAYHYLQVPGGGGEWSTTLL
CPSLGVGTDTNYVKRGSWSTLT.SHAHEVCQKTSAT.DKS.LK.KSCHQGLAYHY.QVPGGG.E.STT.L
RetrocopyCPSLGVGTDTNYVKRGSWSTLTISHAHEVCQKTSATFDKSVLKPKSCHQGLAYHYPQVPGGG-ECSTTML
ParentalSPRETDAAAEGPIPCRRMRSGSYIKAMGDEDSDESGGSPKPSPKTAARRQSYLRATQQSLGEQSNPRRSL
SPRETDAAA.GP.P.R.MRS.SYIKAMGD.DSDESG.SP.PSPKTAARRQSYL..TQ.SLGEQSNP.RSL
RetrocopySPRETDAAAKGPSPFRLMRSSSYIKAMGDKDSDESGRSPEPSPKTAARRQSYLKVTQPSLGEQSNPHRSL
ParentalDRLDSVDMLLPSKCPSWEEDYTPVSDSLNDSSCISQIFGQASLIPQLFGHEQQVREAELSDQYEAACESA
DRLDSVDMLLPSKCP.WEEDY.PVSDSLNDSSCISQIFGQASLIP.LFGHEQQVREAE.S...EAACESA
RetrocopyDRLDSVDMLLPSKCPGWEEDYMPVSDSLNDSSCISQIFGQASLIP*LFGHEQQVREAEPSEPDEAACESA
ParentalCSEAESTAAETLDLPLPSYFRSRSHSYLRAIQAGCSQEEDSVSLQSLSPPPSTGSLSNSRTLPSSSCLVA
CSEAESTAAE.LDLPLPS.FRSRS.SYLRAIQAGCSQEEDSVSLQSLSPPP.T.SLSNS..LPSSSCLVA
RetrocopyCSEAESTAAEMLDLPLPSCFRSRSPSYLRAIQAGCSQEEDSVSLQSLSPPPGTSSLSNSCSLPSSSCLVA
ParentalYKKTPPPVPPRTTSKPFISVTVQSSTESAQDTYLDSQDHKSEVTSQSGLSNSS
YKKT.PPVPP.TTSKPFISVTVQS.TESAQDTYLDSQDHKSEVTSQ.GLSNSS
RetrocopyYKKTLPPVPPCTTSKPFISVTVQSGTESAQDTYLDSQDHKSEVTSQLGLSNSS

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 .50 RPM 74 .31 RPM
SRP007412_cerebellum 0 .12 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_3555 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3555 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3555 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,


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