RetrogeneDB ID:

retro_pabe_1314

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:15:77049291..77050520(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TFDP1
Ensembl ID:ENSPPYG00000025889
Aliases:None
Description:transcription factor Dp-1 [Source:HGNC Symbol;Acc:11749]


Retrocopy-Parental alignment summary:






>retro_pabe_1314
ATGGCAAAAGATGCCGGTCTAATTGAAGCCAACGGAGAACTCAAGATCTTCATAGACCAGAATCTTAGTCCCGGAAAAGG
CGTGGTGTCCCTCGTGGCCGTTCACTCCTCCACTGTCAACCCGCTCGGGGAGCAGCTCTTGGCAACAACCTTTGAACAGT
CCAATGTCAACATTGCCCAGCAAGTGGTAATTGGTGCGCCTCAGAGACGGGCAGCGTCAAACGCCTTGGGGGTAGGAAGC
CCACACACCCCCAGCACTCACTTTGCCGCTCAGAACCAGCCTTCCTACTCCTCACCTTGGTCTGCCGGGAAGCGCAACAG
AAAAGGAGAGAAGAATGGCAGGGGCCTGCGGCATTTCTCCATGAAGGTCTGCGAGAAGGTGCAGAGGAAAGGGACCGCTT
CCTACAACGAAGCGGCAGACGAGCTGGTCGCGGAGTTCAGTGCTGCCGACAACCACATCTTACCAAACGAGTCAGCTTAT
GACCAGAAGAACATAAGACGGCGCGTCTACGATGCCTTAAACGTGCTGATGGCCGTGAACATCATCTCCAAGGAGAAAAA
GGAGGTCAAGTGGATTGGTCTGCCCACCAACTCGGCATAGGAATGTCAGAACTTAGAGGTGGAAAGACAGAGGAGACTTG
AAAGAATAAAACAGAAACAGTCTCAACTTCAAAACTTATTCTACAGCAAATTACCTTCAAGAAACTGGTGCAGAGAAACC
GGCACGCGGAGCAGTAGGCCAGCCAGCCGCCGCCAGCCAACTCGGTCATCCACCTGCCCTTCATCATCATCAACACCAGC
AAGCAGACGGTCATCGACTGCAGCATCTCCAACGACAAATTCGAGTATCTATTTAATTTTGACAACACATTTGAAATCCA
CGATGACATAGAAGTGCTGAAGCGGATGGGCATGCCCTACGGGCTGGAGTCCAGGAGCTGCTCTGCTGAAGACTTTAAAA
TGGCCAGAAGTCTGGTCCCAAAGACTCTGGAGCCGTACGTGACAGAAATGGCTCAGGGAACTGTTGGAGGCGTGTTCATC
GCGACGGCAGGTTCCACGTCTAACGGCACGAGGTTCTCTGCCAGTGACCTGACCAATGGTGCAGATGGGATACTGGCCAC
AAGTTCTAATGGGTCTCAGTACAGCAGCTCCAGGGTGGAGACCCCGGTGTATTACGTCAGGGAGGACGACGAGGAGGATA
ATGACTTCAACGAGAATGAGGAGGACGAC

ORF - retro_pabe_1314 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.51 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAKDAGLIEANGELKVFIDQNLSPGKGVVSLVAVHPSTVNPLGKQLLPKTFGQSNVNIAQQVVIGTPQRP
MAKDAGLIEANGELK.FIDQNLSPGKGVVSLVAVH.STVNPLG.QLL..TF.QSNVNIAQQVVIG.PQR.
RetrocopyMAKDAGLIEANGELKIFIDQNLSPGKGVVSLVAVHSSTVNPLGEQLLATTFEQSNVNIAQQVVIGAPQRR
ParentalAASNTLVVGSPHTPSTHFASQNQPSDSSPWSAGKRNRKGEKNGKGLRHFSMKVCEKVQRKGTTSYNEVAD
AASN.L.VGSPHTPSTHFA.QNQPS.SSPWSAGKRNRKGEKNG.GLRHFSMKVCEKVQRKGT.SYNE.AD
RetrocopyAASNALGVGSPHTPSTHFAAQNQPSYSSPWSAGKRNRKGEKNGRGLRHFSMKVCEKVQRKGTASYNEAAD
ParentalELVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEVERQ
ELVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMA.NIISKEKKE.KWIGLPTNSA.ECQNLEVERQ
RetrocopyELVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMAVNIISKEKKEVKWIGLPTNSA*ECQNLEVERQ
ParentalRRLERIKQKQSQLQ-ELILQQIAFKNLVQRNRHAEQQASRPPPPNSVIHLPFIIVNTSKKTVIDCSISND
RRLERIKQKQSQLQ..LILQQI.FK.LVQRNRHAEQ.AS.PPP.NSVIHLPFII.NTSK.TVIDCSISND
RetrocopyRRLERIKQKQSQLQ<KLILQQITFKKLVQRNRHAEQ*ASQPPPANSVIHLPFIIINTSKQTVIDCSISND
ParentalKFEYLFNFDNTFEIHDDIEVLKRMGMACGLESGSCSAEDLKMARSLVPKALEPYVTEMAQGTVGGVFITT
KFEYLFNFDNTFEIHDDIEVLKRMGM..GLES.SCSAED.KMARSLVPK.LEPYVTEMAQGTVGGVFI.T
RetrocopyKFEYLFNFDNTFEIHDDIEVLKRMGMPYGLESRSCSAEDFKMARSLVPKTLEPYVTEMAQGTVGGVFIAT
ParentalAGSTSNGTRFSASDLTNGADGMLATSSNGSQYSGSRVETPVSYVGEDDEEDDDFNENDEDD
AGSTSNGTRFSASDLTNGADG.LATSSNGSQYS.SRVETPV.YV.EDDEED.DFNEN.EDD
RetrocopyAGSTSNGTRFSASDLTNGADGILATSSNGSQYSSSRVETPVYYVREDDEEDNDFNENEEDD

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 .06 RPM 20 .68 RPM
SRP007412_cerebellum 0 .00 RPM 34 .05 RPM
SRP007412_heart 0 .00 RPM 16 .50 RPM
SRP007412_kidney 0 .00 RPM 21 .74 RPM
SRP007412_liver 0 .03 RPM 11 .23 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1314 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1314 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1314 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000044678 retrocopies
Callithrix jacchus ENSCJAG000000069502 retrocopies
Homo sapiens ENSG000001981764 retrocopies
Gorilla gorilla ENSGGOG000000049082 retrocopies
Loxodonta africana ENSLAFG000000079271 retrocopy
Myotis lucifugus ENSMLUG000000121651 retrocopy
Macaca mulatta ENSMMUG000000074231 retrocopy
Mus musculus ENSMUSG000000384822 retrocopies
Nomascus leucogenys ENSNLEG000000008493 retrocopies
Otolemur garnettii ENSOGAG000000035321 retrocopy
Pongo abelii ENSPPYG00000025889 3 retrocopies
retro_pabe_1314 , retro_pabe_132, retro_pabe_378,



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