RetrogeneDB ID:

retro_ptro_307

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:1:65576433..65577914(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC2A3
Ensembl ID:ENSPTRG00000004626
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_307
GGGACATAGAAGGTCACCCCATCTCTGATCTTCGCCATCACAATTGCTACAATCGGCTCTTTCCAATTTGGCTACAACAC
TGGGGTCATCAATGCTCCTGAGATGATCGTAAGGGAATTTATCAACACTTTGAAGGACAAGGCAAATACCCCTCCCTCTG
AGACATTGCGCTTGTCCCTTTGGTGCTTGTCTATGGCCATATTCTCCATTGGTTGTATGATTAGCTCCTTTTCTGTTGGA
CTGTTTGTCAACAGCTTTGACAGGCATAATTCAATGCTTACTGTCAACCTGTGGGCTGCCACTGGTGGCTGCCTTATGGG
ACTGTGTAAAGTAGCTGAGTTGGTTGAAATACTGATCCTGGCCTACTTGGTTATTGGCCTCTTCTGCAGACTCTGCACAG
GTTTTGTGCCCACGTACATCGAAGACATCTCACCTATTGCCCTGCAAGTTGTCTTTGGCACTCTCAACCAGCTGGGCATT
GTTGTTGGAATTCTGGTGGCCCAGATCTTTGATCTGGAATTCATCCTGGGGTCCAAAGACCTATGGCCTGTGCTATTAGG
CTTTCCCATCTCTCCTGCTGTGCTACGAAGTGCAGCCCTTCCTTTTTGCCCTGAAAGTCCCAGATTCTTGCTCATTAACA
GAAAAGAAGAGGAGAATGCTAAGGAGATCCTCCAGTGGTTGTGGGGCACCCAGGATGTATCCCAAGACATCCAGGAGATG
AAAGATGAGAGTGCAAGGATGGCACAAGAAAAGCAAGTCACTGTGCTGGAGCTCTTTAGAGTATCCAGCTACCGACAGCC
CATCATCATTTCCATCATGCTCCAGCTCTCTCAGCAGCTCTCTGGAATCAATACTGTGTTCTATTACTCAACAGGAATCT
TTAAGGGTGCAGGTGTTCAAGAGCCCATCTGTGTCACCATTGGTGCGGGTGTGGTTAATACTATCTTCACTATAGTTTCC
CTATTTCTAGTGGAAAGGGCAGTAAGAAGGACTCTACATATGATAGGCCTTGGAGGAATGGCTTTTTGTTCCATCCTCAT
GTCTGTTTGTTTGTTATTGAAGGATGAGTGTAATGGGATAAGCTTTGTCTGTATTGGGGCTATCTTGGTCTTTGTGGTCT
TCTTTGAAATTGGGCCAGACCACATTCCCTGGTTTATTGTGGCTGAACTCTTCAGCCAGGGCCCTGGCCCAGCTGTGATG
GCAGTGGCCGGCTGCTCCACCTGGACCTCCAACTTCCTAGTCAGATTGCTTTTCCCTTCTGCTGCTTACTACTTAGGAGC
CTACGTTTTTATTATCTTCACCGACTTCCTCATTACCTTCTTGATCTTTACCTTCTTCAAAGTCCCTGAGATGTGTTACA
GGACTTTCGAAGATATCACACAGGCCTTTGAGGGGCAGGCACACGATGCAAATAGATCTGGAAGGACTGCGTCATGGAGA
TGAACAGTATCCAGCCTGCTAAGGAGACCACCACCAATGTC

ORF - retro_ptro_307 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.67 %
Parental protein coverage: 99.8 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGTQKVTPALIFAITVATIGSFQFGYNTGVINAPEKIIKEFINKTLTDKGNAPPSEVLLTNLWSLSVAIFS
GT.KVTP.LIFAIT.ATIGSFQFGYNTGVINAPE.I..EFIN.TL.DK.N.PPSE.L...LW.LS.AIFS
RetrocopyGT*KVTPSLIFAITIATIGSFQFGYNTGVINAPEMIVREFIN-TLKDKANTPPSETLRLSLWCLSMAIFS
ParentalIGGMIGSFSVGLFVNRFGRRNSMLIVNLLAVTGGCFMGLCKVAKSVEMLILGRLVIGLFCGLCTGFVPMY
IG.MI.SFSVGLFVN.F.R.NSML.VNL.A.TGGC.MGLCKVA..VE.LIL..LVIGLFC.LCTGFVP.Y
RetrocopyIGCMISSFSVGLFVNSFDRHNSMLTVNLWAATGGCLMGLCKVAELVEILILAYLVIGLFCRLCTGFVPTY
ParentalIGEISPTALRGAFGTLNQLGIVVGILVAQIFGLEFILGSEELWPLLLGFTILPAILQSAALPFCPESPRF
I..ISP.AL...FGTLNQLGIVVGILVAQIF.LEFILGS..LWP.LLGF.I.PA.L.SAALPFCPESPRF
RetrocopyIEDISPIALQVVFGTLNQLGIVVGILVAQIFDLEFILGSKDLWPVLLGFPISPAVLRSAALPFCPESPRF
ParentalLLINRKEEENAKQILQRLWGTQDVSQDIQEMKDESARMSQEKQVTVLELFRVSSYRQPIIISIVLQLSQQ
LLINRKEEENAK.ILQ.LWGTQDVSQDIQEMKDESARM.QEKQVTVLELFRVSSYRQPIIISI.LQLSQQ
RetrocopyLLINRKEEENAKEILQWLWGTQDVSQDIQEMKDESARMAQEKQVTVLELFRVSSYRQPIIISIMLQLSQQ
ParentalLSGINAVFYYSTGIFKDAGVQEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCSTLMTV
LSGIN.VFYYSTGIFK.AGVQEPI..TIGAGVVNTIFT.VSLFLVERA.RRTLHMIGLGGMAFCS.LM.V
RetrocopyLSGINTVFYYSTGIFKGAGVQEPICVTIGAGVVNTIFTIVSLFLVERAVRRTLHMIGLGGMAFCSILMSV
ParentalSLLLKDNYNGMSFVCIGAILVFVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGLLFP
.LLLKD..NG.SFVCIGAILVFV.FFEIGP..IPWFIVAELFSQGP.PA.MAVAGCS.WTSNFLV.LLFP
RetrocopyCLLLKDECNGISFVCIGAILVFVVFFEIGPDHIPWFIVAELFSQGPGPAVMAVAGCSTWTSNFLVRLLFP
ParentalSAAHYLGAYVFIIFTGFLITFLAFTFFKVPETRGRTFEDITRAFEGQAHGADRSG-KDGVMEMNSIEPAK
SAA.YLGAYVFIIFT.FLITFL.FTFFKVPE...RTFEDIT.AFEGQAH.A.RSG.KD.VMEMNSI.PAK
RetrocopySAAYYLGAYVFIIFTDFLITFLIFTFFKVPEMCYRTFEDITQAFEGQAHDANRSG<KDCVMEMNSIQPAK
ParentalETTTNV
ETTTNV
RetrocopyETTTNV

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 .11 RPM 71 .93 RPM
SRP007412_cerebellum 0 .14 RPM 70 .77 RPM
SRP007412_heart 0 .00 RPM 11 .22 RPM
SRP007412_kidney 0 .16 RPM 26 .52 RPM
SRP007412_liver 0 .03 RPM 10 .80 RPM
SRP007412_testis 0 .84 RPM 27 .19 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_307 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_307 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_307 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_401
Gorilla gorilla retro_ggor_398
Pongo abelii retro_pabe_315
Macaca mulatta retro_mmul_502
Parental genes homology:
Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000045562 retrocopies
retro_btau_708, retro_btau_709,
Callithrix jacchus ENSCJAG000000189881 retrocopy
retro_cjac_446,
Cavia porcellus ENSCPOG000000030741 retrocopy
retro_cpor_761,
Cavia porcellus ENSCPOG000000098341 retrocopy
retro_cpor_760,
Cavia porcellus ENSCPOG000000112951 retrocopy
retro_cpor_587,
Felis catus ENSFCAG000000016251 retrocopy
retro_fcat_1924,
Homo sapiens ENSG000000598042 retrocopies
retro_hsap_3983, retro_hsap_401,
Gorilla gorilla ENSGGOG000000168131 retrocopy
retro_ggor_398,
Macaca mulatta ENSMMUG000000004392 retrocopies
retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys ENSNLEG000000269032 retrocopies
retro_nleu_1572, retro_nleu_1904,
Oryctolagus cuniculus ENSOCUG000000085751 retrocopy
retro_ocun_352,
Pongo abelii ENSPPYG000000042351 retrocopy
retro_pabe_315,
Pan troglodytes ENSPTRG000000046241 retrocopy
retro_ptro_2703,
Pan troglodytes ENSPTRG00000004626 1 retrocopy
retro_ptro_307 ,


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