RetrogeneDB ID:

retro_ptro_1450

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:21:5692361..5693944(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC6A6
Ensembl ID:ENSPTRG00000014651
Aliases:None
Description:solute carrier family 6 (neurotransmitter transporter, taurine), member 6 [Source:HGNC Symbol;Acc:11052]


Retrocopy-Parental alignment summary:






>retro_ptro_1450
TTCCTGTTTGGAGCGGCCTGCCTGTGTTTTTCTTGGAGATCATCACAGGCCAGTACACCTCTGAAGGGGGCATCACATAT
TGGGAAAAGATCTGGCACTTGTTCTCTGGCATCGGCTCTGCCTCCATCGTAATTGTGCCCTTCCCGAACGTCCACTACAT
CATCATCCTGGCCTGGGCTACATACTACCTGTTCCAGTCCTTCCAGAAGGAGCTGCCCAGGGCACACTGCAACCACAGCT
GGAACATGCCCCCCTGCATGGAGGACACCATGCGCACGAACGAGAGTGTCTGGATCACCATCAGCTCCACCAACCTTACC
TCCCCTGTCACTGAGTTCTAGGGGCGCAACGTGCTGAGCTTGTCCCCTGGAATCGACCATCCGGGCTCTTTGAAATGGTA
CCTCTCTCTCTGTCTTCTCTTTGTCTGGCTAGCCTGTTTCTTCTGCATCTAGAAGGATGTCAGGTCCACGGGGAAGGTCG
TCTACTTCACAGCCACGTTCCAGTTCGCCATGCTCCTGATGCAGCTGGTCCGAGGGCTGATGCTGCCCGGCATGGGTGCC
GGCATCAATTTTTCTCTGTATCCAGACATCACCTGCCTCGAGGGCGCACAGGTGTGTATTGACGCTACGACCCAGATATT
CTTCTCCTAGGCCATCTGCCTGGGGGCCATGACCTCTCTACGGAGCTACAACAAGTACAAGTACAACTCGTACAGGGACT
GCATGTTGCCTGGATGCCTGAACAGTGGTACCAGTTTTGTGTCTGGCTTTGCAATTTTTTCCATCCTGGACTTCATGGCA
CGAAAGCAAGGGGTGGACATTGCTGATGTGTCTGAGTCAGGCCTGGCCTGGTCTTCGTTGCCTACCCCAAAGCTGTGACA
ATGATGCCATTGCCCACGTTTTCGGTCCCTTTTTGTTGTTGTTGTTGTTGTGCTTCTCTTGCTTGGACTGGATGACCAGT
TTGTTGAAGTCAAAGGGGAGATCACGTCCTTGGTTGATCTTTACCCATCCTTCCTAAGGAAAGGTTATCGTCGGGAAATC
TGCACCGCCTTCGTGTGTAGCATCAGCTGCCTGCTGGGGCTGACAATGGTAACGGAGGTTGGCGTCTATGTCTTTGACTA
CTATGCAGCTAGCGGTGTATGCCTTTTGGGGGCTGCGTTCTTTGACTGTATAGTTATTGCCTGGATATATGGTGTTGATA
ATATTTATGACAGTATTGAGACCGTGATCGGCTATCGGGCCGGGCCCTGGATGAAGTACAGCTGGGCTGTGATCACTCCA
TTTCTCTGTGTTGGATGTTTTATCTTCCCGATCGTCAAGTACATACCCCTGACTTACAACGAAACCTACGTGGACACCAA
CTGGGCCATCGGGCTGGGCTGGAGCCTGGCCCTTTCCTCCAGGTTGTGGGTTCCCTTGGTCATCGTCATCCGCCTCTGCC
AGACCGAGGGACTGTTTCTCGTGAGAGTCAAGTAACTGCTGACCCTGAGGGAACCCAACCGCAGGGCTGTGGGGCGCGAG
GGAGCCACACCCTACAGCTCCCGCTCCGTCATGAGCGGCGCTCTCATGAAACCAACCCACATC

ORF - retro_ptro_1450 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.46 %
Parental protein coverage: 85.3 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalFLFG-SGLPVFFLEIIIGQYTSEGGITCWEKICPLFSGIGYASIVIVSLLNVYYIVILAWATYYLFQSFQ
FLFG.SGLPVFFLEII.GQYTSEGGIT.WEKI..LFSGIG.ASIVIV...NV.YI.ILAWATYYLFQSFQ
RetrocopyFLFG<SGLPVFFLEIITGQYTSEGGITYWEKIWHLFSGIGSASIVIVPFPNVHYIIILAWATYYLFQSFQ
ParentalKELPWAHCNHSWNTPHCMEDTMRKNKSVWITISSTNFTSPVIEFWRRNVLSLSPGIDHPGSLKWDLALCL
KELP.AHCNHSWN.P.CMEDTMR.N.SVWITISSTN.TSPV.EF..RNVLSLSPGIDHPGSLKW.L.LCL
RetrocopyKELPRAHCNHSWNMPPCMEDTMRTNESVWITISSTNLTSPVTEF*GRNVLSLSPGIDHPGSLKWYLSLCL
ParentalLLVWLVCFFCIWKGVRSTGKVVYFTATFPFAMLLVLLVRGLTLPGAGAGIKFYLYPDITRLEDPQVWIDA
L.VWL.CFFCI.K.VRSTGKVVYFTATF.FAMLL..LVRGL.LPG.GAGI.F.LYPDIT.LE..QV.IDA
RetrocopyLFVWLACFFCI*KDVRSTGKVVYFTATFQFAMLLMQLVRGLMLPGMGAGINFSLYPDITCLEGAQVCIDA
ParentalGTQIFFSYAICLGAMTSLGSYNKYKYNSYRDCMLLGCLNSGTSFVSGFAIFSILGFMAQEQGVDIADVAE
.TQIFFS.AICLGAMTSL.SYNKYKYNSYRDCML.GCLNSGTSFVSGFAIFSIL.FMA..QGVDIADV.E
RetrocopyTTQIFFS*AICLGAMTSLRSYNKYKYNSYRDCMLPGCLNSGTSFVSGFAIFSILDFMARKQGVDIADVSE
ParentalSG-PGLAFIAYPKAVTMMPL-PTFWSILFFIM--LLLLGLDSQFVEVEGQITSLVDLYPSFLRKGYRREI
SG.PGL.F.AYPKAVTMMPL.P.F.S........LLLLGLD.QFVEV.G.ITSLVDLYPSFLRKGYRREI
RetrocopySG<PGLVFVAYPKAVTMMPL>PRFRSLXXXXXXXLLLLGLDDQFVEVKGEITSLVDLYPSFLRKGYRREI
ParentalFIAFVCSISYLLGLTMVTEGGMYVFQLFDYYAASGVCLLWVAFFECFVIAWIYGGDNLYDGIEDMIGYRP
..AFVCSIS.LLGLTMVTE.G.YV...FDYYAASGVCLL..AFF.C.VIAWIYG.DN.YD.IE..IGYR.
RetrocopyCTAFVCSISCLLGLTMVTEVGVYV---FDYYAASGVCLLGAAFFDCIVIAWIYGVDNIYDSIETVIGYRA
ParentalGPWMKYSWAVITPVLCVGCFIFSLVKYVPLTYNKTYVYPNWAIGLGWSLALSSMLCVPLVIVIRLCQTEG
GPWMKYSWAVITP.LCVGCFIF..VKY.PLTYN.TYV..NWAIGLGWSLALSS.L.VPLVIVIRLCQTEG
RetrocopyGPWMKYSWAVITPFLCVGCFIFPIVKYIPLTYNETYVDTNWAIGLGWSLALSSRLWVPLVIVIRLCQTEG
ParentalPFLVRVKYLLTPREPNRWA-EREGATPYNSRTVMNGALVKPTHI
.FLVRVK.LLT.REPNR.A..REGATPY.SR.VM.GAL.KPTHI
RetrocopyLFLVRVK*LLTLREPNRRAVGREGATPYSSRSVMSGALMKPTHI

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 .00 RPM 20 .56 RPM
SRP007412_cerebellum 0 .00 RPM 45 .42 RPM
SRP007412_heart 0 .00 RPM 23 .46 RPM
SRP007412_kidney 0 .00 RPM 71 .71 RPM
SRP007412_liver 0 .00 RPM 10 .84 RPM
SRP007412_testis 8 .43 RPM 8 .75 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_1450 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1450 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1450 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2498
Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001313891 retrocopy
retro_hsap_2498,
Pan troglodytes ENSPTRG00000014651 1 retrocopy
retro_ptro_1450 ,


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