RetrogeneDB ID:

retro_ptro_2598

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:7:15167817..15169529(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ATXN2L
Ensembl ID:ENSPTRG00000007938
Aliases:None
Description:ataxin 2-like [Source:HGNC Symbol;Acc:31326]


Retrocopy-Parental alignment summary:






>retro_ptro_2598
CCGCCACCGCAGCAGCAGCACCAGGAGAGGCCGGGGGCCGCTGCCATCGGCAGCGCCAGGGGACAGAGCACAGGAAAGGG
ACCTCCGCAGTCACCTGTGTTTGAAGGCGTCTACAACAATTCCAGAATGCTGCACTTCCTTACAGCTGTTGTGGGCTCCA
CTTGTGATGTAAAGGTGAAAAATGGCACCACCTATGAGGGTATCTTCAAGACGCTGAGCTCAAATTTTGAACTAGCAGAG
GATATTGTACACTAGAAAGCATCTGAGCCAGCAGGTGGCCCTCGTCGGGAGGACACTGTAGACACCATGGTGTTTAAGCC
CAGTGATGTCATGCTTGTTCACTTCCAAAATGCTGACTTCAACTACGCTACTAAAGACAAGTTCACCGATTCAGCCATCG
CCATGAACTCGAAGGGAATGGGGAACACAAAGAGAAGGTGCTTCAGCGCTGGGAGCGGGGCGACAGCAACAGCGACAACT
ACGACCTCGAGTCCAACATGTCCAGTGGATGGGACCCCAGTGAAATGTTGAAGTTCAGTGAGGAGAACTACGGTGTGAAG
ACCACCTATGACAGCAGTCTTTCTCCTTATACGGTGCCCTTAGAAAAGGACAACTCGAACGTTTCAGCTGAGAGCAGCGC
GCGGCCCAGTTGGCTCCAGAGATTGAATCAAGCCCCCAGTACCGCCTGCGGATCGCCATGGAGAGCGACGATGGGCGCAC
TGAAGAGGAGAAGCACAGGGCGGTCCAGCGGCAGGGTTCGGAGCGGGAGAGCCCCAGCTTGGCATCCAGGAAGGGGAAGT
ATATCATCCCTCTGCCTCAACGAGTCCAGGAAGGTCCCCAGGGAGGAGTTTGACGCAGCAGCGCTCTGGGCAGTCAGCCT
GGCCTTAGCAATTTGTCACCTCTTGGCCCTCACCACCTGGACAATAGCAATCCTGGCCCAGGTTCTGAGGCCCGTGGTAT
TAATGGAGGCCCTTCCCACATGTCCCCAAAAGCACAGAGGCCTCTGAGAGGTGCCAAGACTCTTGTCTTCACCCAATAAT
AGGCCTTCCGGAGAAACTTCTGTTCCTCCTCCTGCAGTGGGCCGGATGTATCCCCCGAGTTCTCCCAAGTCTGCTGCCCC
TGCCCCAATCTCACCTTCCTGTCCTGAGCTTTCCATCGGCTTGGCAGTGCCAACCCCTTCAGCCTCCGTCCCTGTGACCT
CATCAGTCTCAGATCCTGGAATGGGCTACATTTCCTCAGCTTCTCCAAAGATCTCCCTGGCCCCCACAGATGTAAAAGAA
CTCTCTACCAAGGAACCTGGGAGAACCCTGGAGCCCCAGTAGCTGGCTCAGATAGCTGAGAAAGTCCCTGGTCTTCAGAA
TGAACAGAAACTATTCCAATTGGAAGAACTGAGAAAGTGTGGGGCCCAGTTTAAGCTTCAGCCCCGTAGTTCCCCTGAGA
ACAGCCTGGATCCTTTTCCTCCCTGGACCTTAAAGGAGGAGGCCAAAGGAAAGGAGGAGGATGATGGTCTGTTGACTTCA
GAGCCCATGGGGTCCCCCGTCTCCTCCAAGACAGAGTCTGTATCGGATAAGGAGGACAAACCACCCCTGGCACCAGCAGG
AGGCACTGAGGGGCCAGAGCCGCCCCTACCACCTTGCCCAAGCCAAACCAGCAGCCTCCCCTTTGGCCTCATCAAAGGAG
AGGACAAGGATGAGGGCCCTATTGCTGAACAA

ORF - retro_ptro_2598 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.06 %
Parental protein coverage: 54.31 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalPGPLATSAAPPGPPAAASPCGQSTGKGPPQSPVFEGVYNNSRMLHFLTAVVGSTCDVKVKNGTTYEGIFK
P.P.......PG..A..S..GQSTGKGPPQSPVFEGVYNNSRMLHFLTAVVGSTCDVKVKNGTTYEGIFK
RetrocopyPPPQQQHQERPGAAAIGSARGQSTGKGPPQSPVFEGVYNNSRMLHFLTAVVGSTCDVKVKNGTTYEGIFK
ParentalTLSSKFELAVDAVHRKASEPAGGPRREDIVDTMVFKPSDVMLVHFRNVDFNYATKDKFTDSAIAMSSKV-
TLSS.FELA.D.VH.KASEPAGGPRRED.VDTMVFKPSDVMLVHF.N.DFNYATKDKFTDSAIAM.SK..
RetrocopyTLSSNFELAEDIVH*KASEPAGGPRREDTVDTMVFKPSDVMLVHFQNADFNYATKDKFTDSAIAMNSKG<
ParentalNGEHKEKVLQRWEGGDSNSDDYDLESDMSNGWDPNEMFKFNEENYGVKTTYDSSLSSYTVPLE-KDNSEE
NGEHKEKVLQRWE.GDSNSD.YDLES.MS.GWDP.EM.KF.EENYGVKTTYDSSLS.YTVPLE.K...E.
RetrocopyNGEHKEKVLQRWERGDSNSDNYDLESNMSSGWDPSEMLKFSEENYGVKTTYDSSLSPYTVPLE<KGQLER
ParentalFRQRELRAAQLAREIESSPQYRLRIAMENDDGRTEEEKHSAVQRQGSGRESPSLASREGKYI-PLPQRVR
F...E.RAAQLA.EIESSPQYRLRIAME.DDGRTEEEKH.AVQRQGS.RESPSLASR.GKYI.PLPQRV.
RetrocopyF-S*EQRAAQLAPEIESSPQYRLRIAMESDDGRTEEEKHRAVQRQGSERESPSLASRKGKYIIPLPQRVQ
ParentalEGPRGGVRCSSSRGGRPGLSSLPPRGPHHLDNSSPGPGSEARGINGGPSRMSPKAQRPLRGAKTL-SSPS
EGP.GGV..SS..G..PGLS.L.P.GPHHLDNS.PGPGSEARGINGGPS.MSPKAQRPLRGAKTL.SSP.
RetrocopyEGPQGGV*RSSALGSQPGLSNLSPLGPHHLDNSNPGPGSEARGINGGPSHMSPKAQRPLRGAKTL>SSPN
ParentalNRPSGETSVPPPPAVGRMYPPRSPKSAAPAPISASCPEPPIGSAVPTSSASIPVTSSVSDPGVGSISPAS
NRPSGETSVPPP.AVGRMYPP.SPKSAAPAPIS.SCPE..IG.AVPT.SAS.PVTSSVSDPG.G.IS.AS
RetrocopyNRPSGETSVPPP-AVGRMYPPSSPKSAAPAPISPSCPELSIGLAVPTPSASVPVTSSVSDPGMGYISSAS
ParentalPKISLAPTDVKELSTKEPGRTLEPQELARIAGKVPGLQNEQKRFQLEELRKFGAQFKLQPSSSPENSLDP
PKISLAPTDVKELSTKEPGRTLEPQ.LA.IA.KVPGLQNEQK.FQLEELRK.GAQFKLQP.SSPENSLDP
RetrocopyPKISLAPTDVKELSTKEPGRTLEPQ*LAQIAEKVPGLQNEQKLFQLEELRKCGAQFKLQPRSSPENSLDP
ParentalFPPRILKEEPKGKEKEVDGLLTSEPMGSPVSSKTESVSDKEDKPPLAPSGGTEGPEQPPPPCPSQTGSPP
FPP..LKEE.KGKE...DGLLTSEPMGSPVSSKTESVSDKEDKPPLAP.GGTEGPE.P.PPCPSQT.S.P
RetrocopyFPPWTLKEEAKGKEED-DGLLTSEPMGSPVSSKTESVSDKEDKPPLAPAGGTEGPEPPLPPCPSQTSSLP
ParentalVGLIKGEDKDEGPVAEQ
.GLIKGEDKDEGP.AEQ
RetrocopyFGLIKGEDKDEGPIAEQ

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 .27 RPM 85 .37 RPM
SRP007412_cerebellum 0 .47 RPM 142 .50 RPM
SRP007412_heart 0 .00 RPM 18 .39 RPM
SRP007412_kidney 0 .03 RPM 53 .01 RPM
SRP007412_liver 0 .10 RPM 55 .91 RPM
SRP007412_testis 0 .63 RPM 419 .11 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_2598 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_2598 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2598 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3820
Gorilla gorilla retro_ggor_2570
Macaca mulatta retro_mmul_1631
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001684881 retrocopy
retro_hsap_3820,
Gorilla gorilla ENSGGOG000000141121 retrocopy
retro_ggor_2570,
Macaca mulatta ENSMMUG000000032981 retrocopy
retro_mmul_1631,
Pan troglodytes ENSPTRG00000007938 1 retrocopy
retro_ptro_2598 ,


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