RetrogeneDB ID:

retro_ogar_3343

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873786.1:20742..22388(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOGAG00000034569
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PDPK1
Ensembl ID:ENSOGAG00000005147
Aliases:None
Description:3-phosphoinositide dependent protein kinase-1 [Source:HGNC Symbol;Acc:8816]


Retrocopy-Parental alignment summary:






>retro_ogar_3343
ACGGTTCCTCTCCAGTCCAGTGTGGTGTGATGTCCCTGCCCCAGTCTCCATCAGCGGTGAGCACTGAGTCCCGCGCGGTT
CCTGGCGTTCCCGGTGGTGAGACAAGACAGGACCCCACCATGGACGGCGCCACCACCGAGGGCCTGGCGGGCGCTTGCTC
CCTGCAGCAGGCTTCCCAGCCACTGCCGCCACCACTGCCCGAGAAGAAACGGCCCCAAGACTTCCAGTTTGGGAAAATTC
TTGGCGAAGGTTCTTTTTCGACAGTTGTCCTGGCTCGAGAACTGGCAACCTCCAGGGAATATGCTATTAAAATTCTAGAG
AAAAAGCATATTATCAAAGAGAACAAGGTACCGTATGTAACCACAGAGCGAGATGTGATGTCGCGCCTGGATCATCCCTT
CTTTGTGAAGCTTTACTTCACGTTTCAGGATGAAAAAAGGCTGTATTTTGGCCTTAGTTATGCTCAAAACGGAGCACTTC
TTAAATACCTTCGCAGAATTGGTTCACTCGATGAGACCTGCGCTCGATTCTACACTGCTGAGATCGTGTCCGCCCTAGAG
TACTTGCACAGCAAGGGCATTATTCATAGGGACTTGAAGCCAGAAAACATTCTGTTAAATGCAGATATGCACATCCAGAT
CACAGATTTTGGAACAGCGAAAGTCTTGTCTCCAGAGAGCAAAGAAGTCAGGGCCTACTCGTTCGTAGGAACAGCACAAT
TCGTCTCTCCTGAGCTGCTCACAGAGAAATCAGCCTGTAAAAGTTCAGATCTTTGGGCTCTTGGATGCATCCTATACCAG
TTTGTGGCAGGCTTCCCACCGTTCCGAGCCGGAAATGAATATCTTGTATTTCAGAAGATCATGAAACTGGACTATGACTT
TCCAGAAAAATTCTTCCCAAAGGCAAGAGATCTCGTGGAAAAACTTCTGGTTTTAGATGCCACGAAGCGGTTAGGCTGTG
AAGAAATGGAAGGGTACGGACCGCTTAAAGCTCATCCGTTCTTTGAGTCCATTACGTGGGAGACTCTGCACCTGCAGACA
CCCCCGAAGCTCACCACTTCCTTACCAGGCGCGTTGGAAGACATCGAGGAGGACTACGGCAACTATGACAATGTCCTGAG
CCAGTTTGCCGGCATACAGGTGTCATCATCTTCCTCCTCCCGCACCTTGTCTCGTCAGGATGCCAAAAGACCCCAGAAGT
CCCGCTGCAGCATAGAACGGTACATCCACATTTTGGACCCTAATTCTCTAGAACTGGACCTACGGTTTTCTGAAGAAGAG
AAGAGGTTACTATTGGAGAAGCAGGCTGGTGGAAACCCTTGGCATCGGTTTGTAGAAAATAATTTAATACTAAAAATGGG
TCCAGTGGATAAGCGAAGGGGGCTGTTTGCACGACGACGACAGTTATTGCTCACAGAAGGGCCACATTTATATTATGTGG
ATCCTGTCAACAAAGTCCTGAAAGGTGAAATTCCGTGGTCGCAAGAACTCCGACCAGAGGCCAAAAATTTTAAAACTTTC
TTTGTTCATACGCCTAACAGGACATATTACCTGATGGATCCGTGTGGGAATGCTCACAAGTGGTGCCAAAAGATCCAGGA
GGTTTGGACAAAGCTATACCAGAGCCACCCGGCTGCTGGCATGCAG

ORF - retro_ogar_3343 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.64 %
Parental protein coverage: 98.21 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTVPIQSSVVLC-SCP-SPSMVRTQTESGTVPGIPGGGSSRQGPTMDGTTAESRPSASSLQHAAQPALQP-
TVP.QSSVV.C.S.P.SPS.V...TES..VPG.PGG...RQ.PTMDG.T.E....A.SLQ.A.QP...P.
RetrocopyTVPLQSSVV*C<SLPQSPSAV--STESRAVPGVPGG-ETRQDPTMDGATTEGLAGACSLQQASQPLPPPL
Parental-RKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFV
..KKRP.DF.FGKILGEGSFSTVVLARELATSREYAIKILEK.HIIKENKVPYVT.ERDVMSRLDHPFFV
RetrocopyPEKKRPQDFQFGKILGEGSFSTVVLARELATSREYAIKILEKKHIIKENKVPYVTTERDVMSRLDHPFFV
ParentalKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILL
KLYFTFQD...LYFGLSYA.NG.LLKY.R.IGS.DETC.RFYTAEIVSALEYLH.KGIIHRDLKPENILL
RetrocopyKLYFTFQDEKRLYFGLSYAQNGALLKYLRRIGSLDETCARFYTAEIVSALEYLHSKGIIHRDLKPENILL
ParentalNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFR
N.DMHIQITDFGTAKVLSPESK..RA.SFVGTAQ.VSPELLTEKSACKSSDLWALGCI.YQ.VAG.PPFR
RetrocopyNADMHIQITDFGTAKVLSPESKEVRAYSFVGTAQFVSPELLTEKSACKSSDLWALGCILYQFVAGFPPFR
ParentalAGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYAPLKAHPFFESITWENLHQQ
AGNEYL.FQKI.KL.YDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGY.PLKAHPFFESITWE.LH.Q
RetrocopyAGNEYLVFQKIMKLDYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESITWETLHLQ
ParentalTPPKLTAYLPAMSEDDEDCYGNYDNLLSQFGCMQVSSSSSSHSLSALDASLPQRSGSNIEQYIHDLDTNS
TPPKLT..LP...ED.E..YGNYDN.LSQF...QVSSSSSS..LS..DA..PQ.S...IE.YIH.LD.NS
RetrocopyTPPKLTTSLPGALEDIEEDYGNYDNVLSQFAGIQVSSSSSSRTLSRQDAKRPQKSRCSIERYIHILDPNS
ParentalFELDLQFSEEEKRLLLEKQAGGNPWHQFVENNLILKMGPVDKRKGLFARRRQLLLTEGPHLYYVDPVNKV
.ELDL.FSEEEKRLLLEKQAGGNPWH.FVENNLILKMGPVDKR.GLFARRRQLLLTEGPHLYYVDPVNKV
RetrocopyLELDLRFSEEEKRLLLEKQAGGNPWHRFVENNLILKMGPVDKRRGLFARRRQLLLTEGPHLYYVDPVNKV
ParentalLKGEIPWSQELRPEAKNFKTFFVHTPNRTYYLMDPSGNAHKWCRKIQEVWRQRYQSHPDAAVQ
LKGEIPWSQELRPEAKNFKTFFVHTPNRTYYLMDP.GNAHKWC.KIQEVW...YQSHP.A..Q
RetrocopyLKGEIPWSQELRPEAKNFKTFFVHTPNRTYYLMDPCGNAHKWCQKIQEVWTKLYQSHPAAGMQ

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






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_3343 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Otolemur garnettii ENSOGAG00000005147 1 retrocopy
retro_ogar_3343 ,


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