RetrogeneDB ID:

retro_ptro_688

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:12:44234486..44236044(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PLEKHA8
Ensembl ID:ENSPTRG00000019036
Aliases:None
Description:Pan troglodytes pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8 (PLEKHA8), mRNA. [Source:RefSeq mRNA;Acc:NM_001199079]


Retrocopy-Parental alignment summary:






>retro_ptro_688
ATGGAGGGGGTGCTGTACAAGTGGACCAACTATCTGAGCGGTTGGCAGCCTTGATGGTTCCTTCTCTGTGGGGGAATATT
GTCCTATTATGATTCTCCTGAAGATGCCTGGAAAGGTTGAAAAGGGAGCATACAAATGGCAGTCTGTGAAATTGAAGTTC
ATTCTGTAGATAATACATGCATGCACCTGATAATCCCCGGGGAACAGTATTTCTACCTGAAGGCCAGAAGTGTGCCTGAA
AGATAGCGGCAGCTGGTGGCCCTGGGATCAGCCGAGGCTTGCCTGACTGACAGTAGGACCCAGAAGGATAAAGAGTTTGC
TGAAAACACTGAAAACTTGAAAACCAAAATGTCAGAACTAAGACTCTGCTGTGACCTCCTTGTTCAGCAAGTAGATAAAA
CAAAAGAAGTGACCACAACTGGTGTGTCCAATTCTGAGGAGGGAATTGATGTGGGAATCAATGCTGAAATCAACCTGTAA
TACTTTTCTGAAGACCTTGGAAGAATGCATGCAGATTGCAAATGCAGCCTTCACCTCTGAGCTGCTCTACCACACTCCAC
CAGGATCACCACAGCTGGCCATGCTCAAGTCCAGCAAGATGAAACATCCTATTATACCAATTCATAATTCATTGGAAAGG
CAAATGGAGTTGAGCACTTGTGAAAATGGATCTTTAAATATGGAAATAAATGGTGAGGAAGAAATCCTAATGAAAAATAA
GAATTCCTTATATTTGAAATCTGCAGAGATAGACTGCAGCATATCAAGTGAGGAAAATACAGATGATAATATAACCGTCC
AAGGTGAAATAATGAAGGAAGATGGAATGGAAAACCTGAAAAATCATGACAATAACTTGTCTCAGTCTGGATCAGACTCA
AGTTGCTCTCCAGAATGCCTCTGGGAGGAAGGCAAAGAAGTTATCCCAACTTTCTTTAGTACCATGAACACAAGCTTTAG
TGACATTGAACTTCTGGAAGACAGTGGCATTCCCACAGAAGCATTCTTGGCATCATGTTGTGCTGTGGTTCCAGTATTAG
ACAAACTTGGCCCTACAGTGTTTGCTCCTGTTAAGATGGATCTTGTTGGAAATATTAAGAAAGTAAATCAGAAGTATATA
ACCAACAAAGAAGAGTTTACCACTCTCCAGAAGATAGTTCTGCACGAAGTGGAGGCGGATGTAGCCCAGGTTAGGAACTC
AGCGACTGAAGCCCTCTTGTGGCTGAAGAGAGGTCTCCAATTTTTTAAGGGATTTTTGACAGAAGTGAAAAATGGGGAAA
AGGATATCCAGACAGCCCTGAATAACGCATATGGTAAAACATTGCGGCAACACCATGGCTGGGTAGTTCGAGGGGTTTTT
GCGTTAGCTTTAAGGACAACTCCATCCTATGAAGATTTTGTGGCCGCGTTAACCATAAAGGAAGGTGACCACCAGAAAGA
AGCTTTCAGTATTGGGATGCAGAGGGACCTCAGCCTTTACCTCCCTGCCATGGAGAAGCAGATGGCCATACTGGACGCTT
TATAAGAGGTCCATGGGCTGGAATCTGATGAGGTGGTA

ORF - retro_ptro_688 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.81 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMEGVLYKWTNYLSGWQPRWFLLCGGILSYYDSPEDAWKGCKGSIQMAVCEIQVHSVDNTRMDLIIPGEQY
MEGVLYKWTNYLSGWQP.WFLLCGGILSYYDSPEDAWKG.KGSIQMAVCEI.VHSVDNT.M.LIIPGEQY
RetrocopyMEGVLYKWTNYLSGWQP*WFLLCGGILSYYDSPEDAWKG*KGSIQMAVCEIEVHSVDNTCMHLIIPGEQY
ParentalFYLKARSVAERQRWLVALGSAKACLTDSRTQKEKEFAENTENLKTKMSELRLYCDLLVQQVDKTKEVTTT
FYLKARSV.ER.R.LVALGSA.ACLTDSRTQK.KEFAENTENLKTKMSELRL.CDLLVQQVDKTKEVTTT
RetrocopyFYLKARSVPER*RQLVALGSAEACLTDSRTQKDKEFAENTENLKTKMSELRLCCDLLVQQVDKTKEVTTT
ParentalGVSNSEEGIDVG-TLLKSTCNTFLKTLEECMQIANAAFTSELLYRTPPGSPQLAMLKSSKMKHPIIPIHN
GVSNSEEGIDVG...LKSTCNTFLKTLEECMQIANAAFTSELLY.TPPGSPQLAMLKSSKMKHPIIPIHN
RetrocopyGVSNSEEGIDVG>SMLKSTCNTFLKTLEECMQIANAAFTSELLYHTPPGSPQLAMLKSSKMKHPIIPIHN
ParentalSLERQMELSTCENGSLNMEINGEEEILMKNKNSLYLKSAEIDCSISSEENTDDNITVQGEIRKEDGLENL
SLERQMELSTCENGSLNMEINGEEEILMKNKNSLYLKSAEIDCSISSEENTDDNITVQGEI.KEDG.ENL
RetrocopySLERQMELSTCENGSLNMEINGEEEILMKNKNSLYLKSAEIDCSISSEENTDDNITVQGEIMKEDGMENL
ParentalKNHDNNLTQSGSDSSCSPECLWEEGKEVIPTFFSTMNTSFSDIELLEDSGIPTEAFLASCYAVVPVLDKL
KNHDNNL.QSGSDSSCSPECLWEEGKEVIPTFFSTMNTSFSDIELLEDSGIPTEAFLASC.AVVPVLDKL
RetrocopyKNHDNNLSQSGSDSSCSPECLWEEGKEVIPTFFSTMNTSFSDIELLEDSGIPTEAFLASCCAVVPVLDKL
ParentalGPTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVEADVAQVRNSATEALLWLKRGLKFLKGFL
GPTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVEADVAQVRNSATEALLWLKRGL.F.KGFL
RetrocopyGPTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVEADVAQVRNSATEALLWLKRGLQFFKGFL
ParentalTEVKNGEKDIQTALNNAYGKTLRQHHGWVVRGVFALALRAAPSYEDFVAALTVKEGDHQKEAFSIGMQRD
TEVKNGEKDIQTALNNAYGKTLRQHHGWVVRGVFALALR..PSYEDFVAALT.KEGDHQKEAFSIGMQRD
RetrocopyTEVKNGEKDIQTALNNAYGKTLRQHHGWVVRGVFALALRTTPSYEDFVAALTIKEGDHQKEAFSIGMQRD
ParentalLSLYLPAMEKQLAILDTLYEVHGLESDEVV
LSLYLPAMEKQ.AILD.L.EVHGLESDEVV
RetrocopyLSLYLPAMEKQMAILDAL*EVHGLESDEVV

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 .11 RPM 12 .96 RPM
SRP007412_cerebellum 0 .04 RPM 23 .98 RPM
SRP007412_heart 0 .17 RPM 6 .41 RPM
SRP007412_kidney 0 .08 RPM 24 .84 RPM
SRP007412_liver 0 .07 RPM 7 .27 RPM
SRP007412_testis 0 .00 RPM 11 .17 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_688 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_688 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_688 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1110
Pongo abelii retro_pabe_919
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001060861 retrocopy
retro_hsap_1110,
Gorilla gorilla ENSGGOG000000060311 retrocopy
retro_ggor_868,
Pongo abelii ENSPPYG000000176821 retrocopy
retro_pabe_919,
Pan troglodytes ENSPTRG000000054311 retrocopy
retro_ptro_41,
Pan troglodytes ENSPTRG00000019036 1 retrocopy
retro_ptro_688 ,


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