RetrogeneDB ID:

retro_ptro_2894

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:9:66250827..66251708(-)
Located in intron of:None
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_2894
ACGCAGTTCAACAAGGGCCCCTCCTACAGGCTCTTGGCGGACGTCCAGAACAGGCTTCTGCCCAAATATGACTCCCAGAA
GGAGGCAGAGCTCCGCAGCTGGATCAAGGGATTTACTGGCCTCTCCATCCGCCCCGACTTCCAGAAGGGCCTGAAGGACG
GGATTATCTTATGCACACTCGTGAACAAACTGCAGCCGGGCTCAGTCCCCAAGATCAACGGCTTCCGTGTAGAACTGGCA
CTAGCTAGAAAACCTCTCCAACTTCCTCAAGGCCATGGTCAGCTACGGCATGATCCTGTGGACCTATTTGAGGCCAACGA
CCTGTTTGAGAGTGGGAACAATATGCAGGTGCGGGTGTCTCTTCTCGCCCTGGCAGGGAAGGCCAAGACTAAGGGGCTGC
AGAGCGGGGTGGACATCCGTGACAAGTACTCAGAGAAGCAGAACTTCGACTGGCCCATGAAGGCCAGCCAGTGCGTCATC
GAGCTGCAGATTACCAACAAATGTGCCAGCCAGTCAGGCATGACCGCATATGGCACGAAGAGGCATCTCTACACCCCAAG
AACCGCATCCTGCCCCCCATGGACAACTCGACCATCAGCATCCAGATGGGTACAAACAAGTGCGCCAGCCAGGTGGGCAT
GACGGCTCCCGGGACCCAGCGGCACATCTATGACACCAAGTTGGGAATAGACAAGTGTGAGAACTCCTCCATGTCCCTGA
AGATGGGCTACACGCAGGTTGCCAATCACAGCGGCCAGGTTTTTGGCCTAGGCCGACAAATATACGAACCCAAGTACTAG
CCGGGTGGCCCAGTGGCCCACGGGGCTCCCTCGGCCGGCAACAGCCCAGGGCCAGGGGAGGCCCCTTACTACCAGGAGGA
G

ORF - retro_ptro_2894 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.05 %
Parental protein coverage: 91.79 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalTHFNKGPSYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGMSIGTNFQLGLKDGIILCELINKLQPGSVK
T.FNKGPSY.L.A.V.N....KYD.Q.E..LR.WI...TG.SI...FQ.GLKDGIILC.L.NKLQPGSV.
RetrocopyTQFNKGPSYRLLADVQNRLLPKYDSQKEAELRSWIKGFTGLSIRPDFQKGLKDGIILCTLVNKLQPGSVP
ParentalKVN-ESSLNWPQLENIGNFIKAIQAYGM-KPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTID
K.N..S..NW..LEN..NF.KA...YGM..P.D.FEANDLFE.GN..QV...L.ALAG.AKTKG.....D
RetrocopyKIN>ASV*NWH*LENLSNFLKAMVSYGM<DPVDLFEANDLFESGNNMQVRVSLLALAGKAKTKGLQSGVD
ParentalIGVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAGMTAYGTRRHLY-DPKMQTDKPFDQTTISLQM
I..KY.EKQ...FD....KA.Q.VI.LQ..TNKCASQ.GMTAYGT.RHLY..PK.....P.D..TIS.QM
RetrocopyIRDKYSEKQ--NFD-WPMKASQCVIELQI-TNKCASQSGMTAYGTKRHLY<HPKNRILPPMDNSTISIQM
ParentalGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPTE
GTNK.ASQ.GM.APGT.R.IYD.KL......NS..SL.MG...VA...G..V.GLGRQ.Y.PKY...P..
RetrocopyGTNKCASQVGMTAPGTQRHIYDTKLGIDKCENSSMSLKMGYTQVANHSG-QVFGLGRQIYEPKY--*PGG
ParentalPVIHNGSQGTGTNGSEISDSDYQAE
PV.H.G....G..........YQ.E
RetrocopyPVAH-GAPSAGNSPGPGEAPYYQEE

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 .07 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_2894 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2894 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2894 has 0 orthologous retrocopies within eutheria group .


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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