RetrogeneDB ID:

retro_xmac_10

Retrocopy
location
Organism:Platyfish (Xiphophorus maculatus)
Coordinates:JH556696.1:509337..511458(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSXMAG00000019568
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC5A3 (2 of 2)
Ensembl ID:ENSXMAG00000002730
Aliases:None
Description:solute carrier family 5 (sodium/myo-inositol cotransporter), member 3 [Source:HGNC Symbol;Acc:11038]


Retrocopy-Parental alignment summary:






>retro_xmac_10
ATGCAGGCCAGGATGGAAGCAGCGGACATTGCAGTGGTCGCACTGTATTTTGTCCTGGTGCTGGCCATCGGGCTTTTGGC
CATGTGGAAAGCCAATCGCAGCACCGTGAGTGGCTACTTCCTCGCTGGACGCTCCATGAACTGGGTAGTGATAGGGGCGT
CCCTCTTCGTCAGCAACATTGGCAGCGAACACTTCATAGGTCTGGCTGGGTCGGGTGCAGCAAGCGGCTTTGCTGTAGGA
GCCTGGGAATTCAATGCACTCCTCCTTCTGCAGCTGCTCGGCTGGGTGTTTGTCCCCGTCTACATCTACTCTGGAGTTTA
CACTATGCCAGCGTACCTGTCAAAACGTTTTGGTGGGCACAGGCTGAAGGTTTACTTCGCCTGCCTATCTGTGCTGCTCT
ACGTCTTCACCAAGCTCTCCGTGGATCTGTATGCTGGTGCTCTCTTTATTCAGGAGTCCTTGGGGTGGAACCTTTATCTT
TCAATTCTTCTGCTCATCAGTATGACTGCTCTTCTCACCATCACTGGTGGATTGGTTGCAGTGCTCTACACAGATGCTCT
TCAGGCAGTGCTGATGATTGGTGGAGCCCTGACCTTAACCATCATGAGCCTAATCAAAGTTGGTGGACTAGAAGGGGTCA
GAACTAAGTATATGCAAGCCATTCCTAATGTCACTGCAATAATGGCTGCTGGAAACTACACATATTCACCATCTTGTCGC
ACTGAACCAAAGCCAAACTCACTACGCATCCTTCGCGGCCCTCTAGATGAGGATATTCCTTGGCCAGGTTTCATTCTGGG
GCAAACCCCTGCATCCATTTGGTACTGGTGTGCAGACCAGGTCATTGTGCAGAGAGTATTAGCTGCTAAGAACATTGCTC
ATGCTAAGTGCTCAACACTCATGGCTGGATTTCTCAAGATCCTGCCCATGTTTGTGATAGTCATTCCAGGAATGATCTCT
CGCATCTTATTCGCAGATGAGATTGCCTGCATCGGGCCGGAGCACTGCATGGCTGTGTGCGGTTCCCAGGCTGGGTGCTC
GAACATCGCTTACCCACGCCTGGTGATGGCGGTGATGCCGGTGGGTCTCAGGGGTCTTATGATGGCGGTCATGATTGCTG
CTTTGATGAGTGACCTTGACTCAATCTTCAACAGCGCAAGTACTATCTTCACCCTGGACATCTACCAGACTGTCCGGAAA
ACAGCTACGCAACGCGAGCTGCTGATTGTAGGCCGCATGTTTGTTGTGGTCATGGTGGTAATCAGCATCGCTTGGGTCCC
TGTAATCATTGAGATGCAAGGTGGACAGACATACATGTACATCCAAGAAGTTGCTGGCTATCTCACCCCACCAATAGCTG
CCCTTTTCCTGCTCGGTGTGTTCTGGAAGAGGTGTAACGAGACGGGCGCCTTCTGGGGAGGGATGACGGGTTTCGTGCTC
GGTGCCGTACGGCTGATCCTCGCCTTCTTTTACCGCCAGCCTCGCTGTGACCAGCCAGACAACAGACCCTTCTTCATCGT
CCACATTCATTACATGTACTTTGCAGCTGGACTCTTCTGGATTTCAGGGTTGGTTGCTGTGGTGGTCAGTCTTTGTACCT
CTGCACCGGATGATGAACAGGTGCGCACCGCCACAGTCTGGGGGCTCCGCAAGCTGGAAAAGGTTCCCCCGAAGGACAGA
GCTGTAAAGTACGGTCTCACAGAGAAGAACCCGTGCAACAGCAGCGAAGTCTACTATAAAGACATTCCTGTAGATGTCAA
AATGGATAGGTGTCTAGATGGAGCTGAGATCAAGCTTCTGGTCCCATCCACAGACCATGATCCAGCTACTCCCAGCACGG
AAACGTCCCCTGCCTCCACCCCTGCTGAGCAGCCTGCTTTCAACCAGATGGATATGATCAGACCAGAGCCAGGAGAAAAA
GGCCTGTGCATGCGCTTTATTGACCGTTTCTGTGGGTACAAAGAAGAACCACATGGTGCTCCGCAGAAAATCTCGCAGGA
AGATGAGCGGGTGATTGCAGCGATGCTGTACGAATCCCCCAGAGTTAAACTCCTTCTCAACCTGGCCCTATTTGTGGTCT
GCTCTGTGGGCATATTCATGTTTGTGTACTTCTCACTGTAG

ORF - retro_xmac_10 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.15 %
Parental protein coverage: 76.76 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalATMEAADIVVIVIYFILVLGIGFAAMRKSNRDTVSGYFLAGRSMNWFAVGASLFVSNIGTEHFIGLAGSG
A.MEAADI.V...YF.LVL.IG..AM.K.NR.TVSGYFLAGRSMNW...GASLFVSNIG.EHFIGLAGSG
RetrocopyARMEAADIAVVALYFVLVLAIGLLAMWKANRSTVSGYFLAGRSMNWVVIGASLFVSNIGSEHFIGLAGSG
ParentalAASGFSVAAWEFNALLLLQLLGWVFIPVYIHCQVYTMPEYLCKRFGGKRLKVYFAALTLVLYIFTKLSVD
AASGF.V.AWEFNALLLLQLLGWVF.PVYI...VYTMP.YL.KRFGG.RLKVYFA.L...LY.FTKLSVD
RetrocopyAASGFAVGAWEFNALLLLQLLGWVFVPVYIYSGVYTMPAYLSKRFGGHRLKVYFACLSVLLYVFTKLSVD
ParentalLYSGALFIQESLGWNLYVSIIVLIVMTAALTVTGGLVAVIYTDTVQAIMMIVGALCLTGIGFAKVGGLEG
LY.GALFIQESLGWNLY.SI..LI.MTA.LT.TGGLVAV.YTD..QA..MI.GAL.LT.....KVGGLEG
RetrocopyLYAGALFIQESLGWNLYLSILLLISMTALLTITGGLVAVLYTDALQAVLMIGGALTLTIMSLIKVGGLEG
ParentalLKEKYMQASPNITAILLSSPNLTYSESCKHHLHPKANALKILRGPKDPDLPWPGFLLGQTPASIWYWCAD
...KYMQA.PN.TAI.....N.TYS.SC.....PK.N.L.ILRGP.D.D.PWPGF.LGQTPASIWYWCAD
RetrocopyVRTKYMQAIPNVTAIMAAG-NYTYSPSCR--TEPKPNSLRILRGPLDEDIPWPGFILGQTPASIWYWCAD
ParentalQVIVQRVLAAKNIVHAKGSTIMAGFLKTLPMFVMVMPGMISRVLFTDQLACIGPDHCMQVCGSAAGCSNV
QVIVQRVLAAKNI.HAK.ST.MAGFLK.LPMFV.V.PGMISR.LF.D..ACIGP.HCM.VCGS.AGCSN.
RetrocopyQVIVQRVLAAKNIAHAKCSTLMAGFLKILPMFVIVIPGMISRILFADEIACIGPEHCMAVCGSQAGCSNI
ParentalAYPRLVMSVMPVGLRGLMMAAMIAALMSDLDSIFNSASTIFTLDIYKMLRKDTSPKELVITGRLFVILMV
AYPRLVM.VMPVGLRGLMMA.MIAALMSDLDSIFNSASTIFTLDIY...RK.....EL.I.GR.FV..MV
RetrocopyAYPRLVMAVMPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDIYQTVRKTATQRELLIVGRMFVVVMV
ParentalALSIAWVPVVIEMQGGQMFYYIQEVSDYLTPPVAALFLLGVLWQRCNETGAFWGGVVGSALGALRLLLAV
..SIAWVPV.IEMQGGQ...YIQEV..YLTPP.AALFLLGV.W.RCNETGAFWGG..G..LGA.RL.LA.
RetrocopyVISIAWVPVIIEMQGGQTYMYIQEVAGYLTPPIAALFLLGVFWKRCNETGAFWGGMTGFVLGAVRLILAF
ParentalVYREPYCGQPDERPSFIKQIHFMYVAAILFWVSAITTIVVSLCTPPPEKQLIRTTTLWGLRQRMK
.YR.P.C.QPD.RP.FI..IH.MY.AA.LFW.S.....VVSLCT..P.....RT.T.WGLR...K
RetrocopyFYRQPRCDQPDNRPFFIVHIHYMYFAAGLFWISGLVAVVVSLCTSAPDDEQVRTATVWGLRKLEK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Xiphophorus maculatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Xiphophorus maculatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_xmac_10 retrocopy.

TSS - click to see more details

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_xmac_10 was not experimentally validated.

Retrocopy orthology:
Xiphophorus maculatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Oreochromis niloticus ENSONIG000000152911 retrocopy
retro_onil_23,
Tetraodon nigroviridis ENSTNIG000000145131 retrocopy
retro_tnig_13,
Xiphophorus maculatus ENSXMAG00000002730 1 retrocopy
retro_xmac_10 ,


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