RetrogeneDB ID:

retro_ptro_3107

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:X:41462567..41463323(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CLIC4
Ensembl ID:ENSPTRG00000000350
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_3107
ATGGCGTTGTCGATGCCGTTGAACGGGCTGAAGGAGGAGGACAAAGAGCCCCTCATTGAGCTCCTCGTCAAAGCTGGCAG
TGATGGTGAAAGCATAGGAAACTGCCCCTTTTCCCAGAGGTTCTTCATGATTCGTTGACTCAAAGGAGTTGTATTTAGTG
TCACAACTGTTGACCTGAAATGGAAGCCTGCAGACCTTCAGAACTTAGCTCCCAGGACCCACCCACCGTTTGTAAGTTTC
AACAGTGAAGTCAAAACGGATGTAAGTAAGATTGAGGAATTTCTTGAAGAAGTCTTACGCCCTCCCAAGTACTTAAAGCT
TTCACCAAAACACCCAGAATCAAATACTGCTGGAATGGACATCTTTGCCAAATTCTCTGCATTTATCAAGAATTGAAGGC
GAGAGGCTAATGAAGCACTGGAGAAGGATCTCCTGAAAACCCTGCAGAAACTGGATAAATATCTGAATTCTCCTCTCCCT
GATGAAATTGATGAAAATAGTATAGAGGACATTAAGTTTTCTACACATAAATTTCTGGATGGCAATGAAATGACATTAGC
TGATTGCAGCCTGCTCCCCAAACTGCATATTGTCAAGGTGGTGGCCAAAAAATATCACAACTTTGATATTCCAAAAGAGA
TGACTGGCATCTGGAGATACCTAACTAATGCATATAGTAGGGACGAGTTCATCAATACCTGTCCCAGTGATAAGGAGGTT
GAAATAGCATATAGTGATGCCAAAAGACCCACCAAG

ORF - retro_ptro_3107 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.91 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMALSMPLNGLKEEDKEPLIELFVKAGSDGESIGNCPFSQRLFMILWLKGVVFSVTTVDLKRKPADLQNLA
MALSMPLNGLKEEDKEPLIEL.VKAGSDGESIGNCPFSQR.FMI..LKGVVFSVTTVDLK.KPADLQNLA
RetrocopyMALSMPLNGLKEEDKEPLIELLVKAGSDGESIGNCPFSQRFFMIR*LKGVVFSVTTVDLKWKPADLQNLA
ParentalPGTHPPFITFNSEVKTDVNKIEEFLEEVLCPPKYLKLSPKHPESNTAGMDIFAKFSAYIKNSRPEANEAL
P.THPPF..FNSEVKTDV.KIEEFLEEVL.PPKYLKLSPKHPESNTAGMDIFAKFSA.IKN.R.EANEAL
RetrocopyPRTHPPFVSFNSEVKTDVSKIEEFLEEVLRPPKYLKLSPKHPESNTAGMDIFAKFSAFIKN*RREANEAL
ParentalERGLLKTLQKLDEYLNSPLPDEIDENSMEDIKFSTRKFLDGNEMTLADCNLLPKLHIVKVVAKKYRNFDI
E..LLKTLQKLD.YLNSPLPDEIDENS.EDIKFST.KFLDGNEMTLADC.LLPKLHIVKVVAKKY.NFDI
RetrocopyEKDLLKTLQKLDKYLNSPLPDEIDENSIEDIKFSTHKFLDGNEMTLADCSLLPKLHIVKVVAKKYHNFDI
ParentalPKEMTGIWRYLTNAYSRDEFTNTCPSDKEVEIAYSDVAKRLTK
PKEMTGIWRYLTNAYSRDEF.NTCPSDKEVEIAYSD.AKR.TK
RetrocopyPKEMTGIWRYLTNAYSRDEFINTCPSDKEVEIAYSD-AKRPTK

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 36 .27 RPM
SRP007412_cerebellum 0 .11 RPM 19 .68 RPM
SRP007412_heart 0 .03 RPM 182 .69 RPM
SRP007412_kidney 0 .05 RPM 200 .61 RPM
SRP007412_liver 0 .00 RPM 30 .70 RPM
SRP007412_testis 0 .00 RPM 52 .59 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3107 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3107 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3107 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 17 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000000759110 retrocopies
Callithrix jacchus ENSCJAG000000208332 retrocopies
Cavia porcellus ENSCPOG000000040101 retrocopy
Homo sapiens ENSG000001695042 retrocopies
Gorilla gorilla ENSGGOG000000055862 retrocopies
Macropus eugenii ENSMEUG000000087891 retrocopy
Macaca mulatta ENSMMUG000000024162 retrocopies
Mus musculus ENSMUSG000000372422 retrocopies
Nomascus leucogenys ENSNLEG000000089973 retrocopies
Otolemur garnettii ENSOGAG000000146201 retrocopy
Pongo abelii ENSPPYG000000017153 retrocopies
Pan troglodytes ENSPTRG00000000350 3 retrocopies
retro_ptro_2816, retro_ptro_3107 , retro_ptro_396,
Pan troglodytes ENSPTRG000000179822 retrocopies
Pteropus vampyrus ENSPVAG000000058381 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000021841 retrocopy
Tarsius syrichta ENSTSYG000000089781 retrocopy
Vicugna pacos ENSVPAG000000076991 retrocopy



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