RetrogeneDB ID:

retro_ptro_2975

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:GL389721.1:2833..3555(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KIAA1191
Ensembl ID:ENSPTRG00000017558
Aliases:None
Description:KIAA1191 [Source:HGNC Symbol;Acc:29209]


Retrocopy-Parental alignment summary:






>retro_ptro_2975
ATGGCTTCAAGACAACCAGAAGTGCCTGCTCTTGAGGCTAGTGGGCCTCTAGGCAAGATGTCCCTGCCCTTCGGGATATA
CCGCCGGGCACTCAGGTATGATGATACCCTCAAGGACCCTGCACCCATGACTCCTCCTCCATCAGACATGGGCAGCATCC
CTTGGAAGCCAGTGATTTCAGAGCGCAAGTATCAGCACCTCACCAAGGTGGAGGAAGGAGAGGCCAGTCTACCCTCCCCT
GCCGGTCCCTGTCATCGGCCATTGACAGTGTGGACAAGGTCCCAGTGGTGAAGGCTAAAGCTACCCATGTCGTCATGAAT
TATATGATCACAAAACAGACCCAGGAAAGCTTTCAGCATTTTGGGCGACAGGCAGGGCTGAGAGATGCTGGCTACACACC
CCACGAGGGTGTCACCACTCAGAAGACCAAGTACCTTAGAGTAGCAGAAGCACTCCACAAACTAAAGCTCCAGAGTGGAG
AGATAACAAAAGAAGAGAGGCCGCCTGCATCAGCCCTGTCCACCCCAAGCACCACTTCTCACTTTTCACCTAAGCAGAGA
CCCAGGGGCTGGTTCACTTCTGGTTCTTCCACAGCCTTACCTGGCCCAAATCCTAGCACCATGGACTCTGGAAGTGGGGA
TAAGGACAGAAACTTGTCAGGTAAGTGGGGCCTCTTTGGACCGAGATCCCTTCAGAAGTATGATTCTGGAAGTTTTGCCA
CC

ORF - retro_ptro_2975 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.67 %
Parental protein coverage: 79.02 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMASRQPEVPALEASAPLGKMSLPIGIYRRALSYDDTLEDPAPMTPPPSDMGSVPWKPVIPERKYQHLAKV
MASRQPEVPALEAS.PLGKMSLP.GIYRRAL.YDDTL.DPAPMTPPPSDMGS.PWKPVI.ERKYQHL.KV
RetrocopyMASRQPEVPALEASGPLGKMSLPFGIYRRALRYDDTLKDPAPMTPPPSDMGSIPWKPVISERKYQHLTKV
ParentalEEGEASLPSPA-MTLSSAIDSVDKVPVVKAKATHVIMNSLITKQTQESIQHFERQAGLRDAGYTPHKGLT
EEGEASLPSPA...LSSAIDSVDKVPVVKAKATHV.MN..ITKQTQES.QHF.RQAGLRDAGYTPH.G.T
RetrocopyEEGEASLPSPA<RSLSSAIDSVDKVPVVKAKATHVVMNYMITKQTQESFQHFGRQAGLRDAGYTPHEGVT
ParentalTEETKYLRVAEALHKLKLQSGEITKEERQPASAQSTPSTTPHSSPKQRPRGWFTSGSSTALPGPNPSTMD
T..TKYLRVAEALHKLKLQSGEITKEER.PASA.STPSTT.H.SPKQRPRGWFTSGSSTALPGPNPSTMD
RetrocopyTQKTKYLRVAEALHKLKLQSGEITKEERPPASALSTPSTTSHFSPKQRPRGWFTSGSSTALPGPNPSTMD
ParentalSGSGDKDRNLSDKWSLFGPRSLQKYDSGSFAT
SGSGDKDRNLS.KW.LFGPRSLQKYDSGSFAT
RetrocopySGSGDKDRNLSGKWGLFGPRSLQKYDSGSFAT

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 .00 RPM 77 .99 RPM
SRP007412_cerebellum 0 .00 RPM 80 .30 RPM
SRP007412_heart 0 .00 RPM 25 .65 RPM
SRP007412_kidney 0 .03 RPM 338 .38 RPM
SRP007412_liver 0 .00 RPM 28 .58 RPM
SRP007412_testis 0 .00 RPM 12 .01 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2975 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2975 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2975 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 25 parental genes, and 64 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000061234 retrocopies
Callithrix jacchus ENSCJAG000000123372 retrocopies
Cavia porcellus ENSCPOG000000194021 retrocopy
Dasypus novemcinctus ENSDNOG000000026763 retrocopies
Equus caballus ENSECAG000000032381 retrocopy
Felis catus ENSFCAG000000071891 retrocopy
Homo sapiens ENSG000001222034 retrocopies
Gorilla gorilla ENSGGOG000000238344 retrocopies
Loxodonta africana ENSLAFG000000288781 retrocopy
Myotis lucifugus ENSMLUG000000034981 retrocopy
Macaca mulatta ENSMMUG000000039213 retrocopies
Monodelphis domestica ENSMODG000000052746 retrocopies
Mustela putorius furoENSMPUG000000125791 retrocopy
Mus musculus ENSMUSG000000258712 retrocopies
Nomascus leucogenys ENSNLEG000000124734 retrocopies
Oryctolagus cuniculus ENSOCUG000000121913 retrocopies
Otolemur garnettii ENSOGAG000000082816 retrocopies
Procavia capensis ENSPCAG000000088391 retrocopy
Pongo abelii ENSPPYG000000160684 retrocopies
Pan troglodytes ENSPTRG00000017558 5 retrocopies
Pteropus vampyrus ENSPVAG000000124481 retrocopy
Rattus norvegicus ENSRNOG000000171332 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000009462 retrocopies
Tupaia belangeri ENSTBEG000000131891 retrocopy
Tursiops truncatus ENSTTRG000000053761 retrocopy



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