RetrogeneDB ID:

retro_pabe_1836

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:20_random:4456651..4458102(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KLF4
Ensembl ID:ENSPPYG00000019478
Aliases:None
Description:Kruppel-like factor 4 (gut) [Source:HGNC Symbol;Acc:6348]


Retrocopy-Parental alignment summary:






>retro_pabe_1836
ATGAGGCAGCCACCTGGCGAGTCTGACATGGCTGTCAGCGACGCGCTGCTCCCATCTTTCTCCACGTTCGCGTCTGGCCC
GGCGGGAAGGGAGAAGACACTGCATCAGGCAGGTACCCCGAATAACCGCTGGCGGGAGGAGCTCTCCCACATGGAGCGAC
TTCCCCCGGTGCTTCCCGGCCGCCCCTATGACCTGGCGGCGGCGACCGTGGCCACAGACCTGGAGAGCGGCGGAGCCGGT
GCGGCTTGCGGCGGTAGCAACCTGGCGCCCCTACCTCGGAGAGAGACCGAGGAGTTCAACGATCTCCTGGACCTGGACTT
TCATCCTCTCCAATTCGCTGACCCATCCTCCGGAGTCAGTGGCCGCCACCGTGTCCTCGTCAGCGTCAGCCTCCTCCTCC
TCCTCGTCGTCCCCGTCGAGCAGCGGCCCTGCCAGCGCGCCCCCCACCTGCAGCTTCACCGATCCCATCCGGGCCGGGAA
ACACCCGGGCGTGGCGCCGGGAGGCACGGGCGGAGGCCTCTTGATGGCAGGGAGTCCGCTCCCCCTCCGACGGCTCCCTT
CAACCTGGCGGACATCAACGACGTGAGCCCCTCGGGCGGCTTCGTGGCCGAGCTCCTGCGGCCAGAATTGGACCCGGTGT
ACATTCCGCCGCAGCAGCCGCAGCCGCCAGGTGCCGGGCTGATGGGCAAGTTCGTGCTGAAGGCGTCGCTGAGCGCCCCT
GGCAGCGAGTGTGCCCGCCCGTCGGTCATCAGCGTCAGCAAAGGCAGCCCTGACGGCAGCCACCCGGTGGTGGTGGCGCC
CTACAAAGGCGGGCCGCCGCGCACATGCCCCAAGATCAAGCGGGAGGCGGTCTCCTCGTGCACTCACTTGGGCGTTGGAC
CCCCTCTCAGCAATGGCCACCGGCCGGCTGCACACGACTTCCCCCTGGGGCGGCAGCTCCCCAGCAGGACTACCCCGACC
CTGGGTCTGGAGGAAGTGCTGAGCAGCCGGGACTGTCACCCTGCCCTGCCGCTTCCCCCCTCCCCCTCCGGCTTCCATCC
CCACCCGGGGCCCAATTACCCATCCTTCCTGCCCGACCAGATGCAGCCGCAAGTCCCGCCGCTCCATTACCAAGAGCTCA
TGCCACCCGGTTCCTGCATGCCGGAGGAGCCCAAGCCAAAGAGGGGAAGACGATCGTGGCCCCGAAAAGGGCCGCCACCC
ACACTTGTGATTACGCGGGCTGCGGCCAAGCCTACACAAAGAGTTCCCATCTCAAGGCACACCTGCGAACCCACACAGGT
GAGAAACCTTACCACTGTGTCTGGGACAGCTGTGGATGGAAATTCGCCCGCTCGGATGAACTGACCAGGCACTACCGTAA
ACACACTGGGCACCGCCCATTCCAGTGCCAAAAATGCGACCGAGCATTTTCCAGGTCGGACCACCTCGCCTTACACATGA
AGAGGCATTTT

ORF - retro_pabe_1836 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.05 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMRQPPGESDMAVSDALLPSFSTFASGPAGREKTLRQAGAPNNRWREELSHMKRLPPVLPGRPYDLAAATV
MRQPPGESDMAVSDALLPSFSTFASGPAGREKTL.QAG.PNNRWREELSHM.RLPPVLPGRPYDLAAATV
RetrocopyMRQPPGESDMAVSDALLPSFSTFASGPAGREKTLHQAGTPNNRWREELSHMERLPPVLPGRPYDLAAATV
ParentalATDLESGGAGAACGGSNLVPLPRRETEEFNDLLDLDF-ILSNSLTHPPESVAATVSSSASASSSSS--PS
ATDLESGGAGAACGGSNL.PLPRRETEEFNDLLDLDF.ILSNSLTHPPESVAATVSSSASASSSSS..PS
RetrocopyATDLESGGAGAACGGSNLAPLPRRETEEFNDLLDLDF>ILSNSLTHPPESVAATVSSSASASSSSSSSPS
ParentalSSGPASAPSTCSFTYPIRAGNDPGVAPGGTGGGLLY-GRESAPPPTAPFNLADINDVSPSGGFVAELLRP
SSGPASAP.TCSFT.PIRAG..PGVAPGGTGGGLL..GRESAPPPTAPFNLADINDVSPSGGFVAELLRP
RetrocopySSGPASAPPTCSFTDPIRAGKHPGVAPGGTGGGLLM<GRESAPPPTAPFNLADINDVSPSGGFVAELLRP
ParentalELDPVYIPPQQPQPPGGGLMGKFVLKASLSAPGSEYGSPSVISVSKGSPDGSHPVVVAPYNGGPPRTCPK
ELDPVYIPPQQPQPPG.GLMGKFVLKASLSAPGSE...PSVISVSKGSPDGSHPVVVAPY.GGPPRTCPK
RetrocopyELDPVYIPPQQPQPPGAGLMGKFVLKASLSAPGSECARPSVISVSKGSPDGSHPVVVAPYKGGPPRTCPK
ParentalIKQEAVSSCTHLGAGPPLSNGHRPAAHDFPLGRQLPSRTTPTLGLEEVLSSRDCHPALPLPP---GFHPH
IK.EAVSSCTHLG.GPPLSNGHRPAAHDFPLGRQLPSRTTPTLGLEEVLSSRDCHPALPLPP...GFHPH
RetrocopyIKREAVSSCTHLGVGPPLSNGHRPAAHDFPLGRQLPSRTTPTLGLEEVLSSRDCHPALPLPPSPSGFHPH
ParentalPGPNYPSFLPDQMQPQVPPLHYQELMPPGSCMPEEPKPKRGRRSWPR-KRTATHTCDYAGCGKTYTKSSH
PGPNYPSFLPDQMQPQVPPLHYQELMPPGSCMPEEPKPKRGRRSWPR.KR.ATHTCDYAGCG..YTKSSH
RetrocopyPGPNYPSFLPDQMQPQVPPLHYQELMPPGSCMPEEPKPKRGRRSWPR<KRAATHTCDYAGCGQAYTKSSH
ParentalLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTGHRPFQCQKCDRAFSRSDHLALHMKRHF
LKAHLRTHTGEKPYHC.WD.CGWKFARSDELTRHYRKHTGHRPFQCQKCDRAFSRSDHLALHMKRHF
RetrocopyLKAHLRTHTGEKPYHCVWDSCGWKFARSDELTRHYRKHTGHRPFQCQKCDRAFSRSDHLALHMKRHF

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 1 .38 RPM
SRP007412_cerebellum 0 .00 RPM 0 .85 RPM
SRP007412_heart 0 .00 RPM 3 .76 RPM
SRP007412_kidney 0 .03 RPM 1 .96 RPM
SRP007412_liver 0 .00 RPM 1 .53 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1836 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1836 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1836 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000203551 retrocopy
Pongo abelii ENSPPYG000000131141 retrocopy
Pongo abelii ENSPPYG00000019478 7 retrocopies
Rattus norvegicus ENSRNOG000000162991 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000220021 retrocopy



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