RetrogeneDB ID:

retro_ptro_1061

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:15:55322044..55322846(-)
Located in intron of:ENSPTRG00000007113
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CNN3
Ensembl ID:ENSPTRG00000000979
Aliases:CNN3, calponin-3
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_1061
TATGGGCTGTCAGCCGAGGTCAAGAACTGGCTCCTGCCCAAATATGACCCCCAGAAGGAGGCAGAGCTCCGCAGCTGGAT
CAAGGGACTCACCGGCATCTCCACTGACCCTGACTTCCAGAAGAGCCTGAAGGACGGGATTATCTTATGCATACTCATGA
ACAAGCTGCAGCCGGCCTCAGTCCCCAAGATCAACCACTCCATGCAGAAGTGGCACCAGCTGGAAAACCTCTCCAACTTC
GTCAAGGCTGTAGTCAGCTATGACATGAACCCCATGGACCTGTTCGAGGCCAACAACCTATTTGAGAGTGGGAACATGAG
GCACATGCAGGTGTCTCTTTTTGCCCTAGCAGGGAAGGTCAAGACTAAGAGGCCACAGAGCGGGGTGGACATTGGCATCA
AGTACTCAGAGAAGCAGGAGCAGAACTTCAGTGACGCCGCCATGAAGGCTGGCCAGTGCGTCATCGGGCTGCAAATGGGC
ACCAACAAATGTACCAGCCAGTTGGGCATGACCGTGTATGGCGTGAGGAGGCATCTGTGTGACCCCAAGAATCACATCCT
GCCCCCCCATGGACCACTCGACCATTGGCCTCCAGATGGGTACAAATAAGTGTGCCAGCCAGGTGAGCATGACAGCTCCT
GGGACGTGGCAGCACATCTATGACACCAAGCTGGGAACCGACAAGTGTGATAATTCCTCCATGTCCCTGCAGATGGGCTA
CACCCAGGGTACCAACCATAGTAGCCAGGTCTTTGGCCTGGGCCAGCATATATGTGACCCCAAGTACTGCCTGCCAGGCA
CA

ORF - retro_ptro_1061 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.25 %
Parental protein coverage: 81.46 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGMSIGTNFQLGLKDGIILCELINKLQPGSVKKVNESSLN
YGLSAEVKN....KYD.Q.E..LR.WI...TG.S....FQ..LKDGIILC.L.NKLQP.SV.K.N.S...
RetrocopyYGLSAEVKNWLLPKYDPQKEAELRSWIKGLTGISTDPDFQKSLKDGIILCILMNKLQPASVPKINHSMQK
ParentalWPQLENIGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTIDIGVKYAEKQT
W.QLEN..NF.KA...Y.M.P.D.FEAN.LFE.GNM...Q..L.ALAG..KTK......DIG.KY.EKQ.
RetrocopyWHQLENLSNFVKAVVSYDMNPMDLFEANNLFESGNMRHMQVSLFALAGKVKTKRPQSGVDIGIKYSEKQE
ParentalRRFDEGKLKAGQSVIGLQMGTNKCASQAGMTAYGTRRHLYDPK-MQTDKPFDQTTISLQMGTNKGASQAG
..F.....KAGQ.VIGLQMGTNKC.SQ.GMT.YG.RRHL.DPK......P.D..TI.LQMGTNK.ASQ..
RetrocopyQNFSDAAMKAGQCVIGLQMGTNKCTSQLGMTVYGVRRHLCDPK>ITSCPPMDHSTIGLQMGTNKCASQVS
ParentalMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPT
M.APGT...IYD.KL.....DNS..SLQMG...........V.GLG....DPKYC...T
RetrocopyMTAPGTWQHIYDTKLGTDKCDNSSMSLQMGYTQ-GTNHSSQVFGLGQHICDPKYCLPGT

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 .02 RPM 37 .13 RPM
SRP007412_cerebellum 0 .04 RPM 64 .38 RPM
SRP007412_heart 0 .00 RPM 25 .77 RPM
SRP007412_kidney 0 .03 RPM 191 .01 RPM
SRP007412_liver 0 .00 RPM 31 .03 RPM
SRP007412_testis 0 .00 RPM 79 .88 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1061 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1061 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1061 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1575
Gorilla gorilla retro_ggor_1199
Pongo abelii retro_pabe_1299

Parental genes homology:
Parental genes homology involve 11 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000181283 retrocopies
Equus caballus ENSECAG000000201881 retrocopy
Echinops telfairi ENSETEG000000100951 retrocopy
Macropus eugenii ENSMEUG000000029212 retrocopies
Monodelphis domestica ENSMODG000000043261 retrocopy
Nomascus leucogenys ENSNLEG000000112075 retrocopies
Pan troglodytes ENSPTRG00000000979 15 retrocopies
Pan troglodytes ENSPTRG000000015331 retrocopy
Sarcophilus harrisii ENSSHAG000000026701 retrocopy
Tarsius syrichta ENSTSYG000000107492 retrocopies
Vicugna pacos ENSVPAG000000048892 retrocopies



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