RetrogeneDB ID:

retro_stub_19

Retrocopy
location
Organism:Potato (Solanum tuberosum)
Coordinates:9:8918339..8920175(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:PGSC0003DMG400040591
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:PGSC0003DMG400029083
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_stub_19
CGAGTGTATTCAATGGAGGATATAAGCTCTCACTATTGTATTAACAGTGGTATTCTTCCTTCTCTTGGCGGCCATAGTGA
TAGCAAAATTAGGCTTCGTAACTACATCATCTCCCCTACTAATCCCCGTTACAAGGTTTGGGACGCATTTTTGGTGCTTC
TTGTTTTCTACACAGCATGGGCATCACCTTTTCAGATTGGATTTCTAGAAACACCTCAAGGACTTATTGCCATCTTAGAT
AACATAGTCAACTTCTTTTTTGCCATTGACATTATCCTCTCATTGTTCTTTGTTGCATATCTTGATAAATCAACTTACAC
TATGATTGATGACCCAAAGCGCATTGCTTTGAGGTATATAAAATATGGATTTATCTTTGATTTCATATCCACTATCCCTT
ACGAAGCATTGCCTCGTATTCTTCAATCATATGGATTCTTGAGTATGCTTCGTCTCTGGCGTCTCAGAAGAGTCAGTGCC
ATGTTTGTCGAATTGGAGAAAAACAACAAGTTGAGTTACTTTGGGATTCGAGTACTCAAGCTTGTATGTGTCACTCTTTT
TGCTGTTCATTCTGCTGGCTGCTTCTACTACTTTCTTGCTGCTCGGATTAAAGACGTTAGTAAAACATGGCTTTCACTGG
GAAATCTTCATGATAGGAGTATCTGGGATCTTTATGTAATGTCTATGTATTGGTCCATTACAACTCTTACAACAACTGGC
TATGGGGATTTGCATGCTGTCACTACAGAGGAAATGATATTCACCATGGTTTACATGTTATTCGACCTCGGGCTGACTGC
ATATCTTATTGGAAACATGACCAACTTGGTTGTCCATGGAACCAATAAGACGCAGAAATTTAGGGATGCTATTCAAGCTG
CCTCAAGCTTTGCACAAAGGAATAATCTGCCTGTTCGACTTGAAGAACAGATGCTAGATCACTTGTCAATGATGCACAGA
ACAGATACGGAAGGTCTGCAGCAGCAAGAAACTCTTGAAACACTACCCAGAGCTATTCGATCTGCCATTTCACATCATCT
ATTCTATTCACTGGTGGATAAGGCCTACTTATTCCAGGGGATATCAAATGACTTACTTTTTCAACTGATTTCTGAGATGA
AGGCCGAGTATTTCCCTCCAAAAGAGGATGTCATTTTGCAAAATGAAGCATCAACAGAACTCTACATCCTCGTAACTGGA
GCAGTGGATCTTATATCACACAAGAATGGTATGGATCATGTAGTTGGCGAGTTGAAGGCAGGGGATGTTTGCGGAGAAGT
TGGTATCCTTTGTTGTAGGCCTCAACTTTTTACTGTTCGAACCAAAAGAATATCCCAACTGCTACGCCTGGATCGTACTT
CATTTTTCAACACCGTTAAAGCAAATAAAGGAGACAGGACAATAATTATGAACAATCTCCTTCAGCATTTGAAAGAGCAA
ACAGACCCAATGATGACTGCAGTATTAGCAGATATAGAACATATCTTCACTCCTGAAGAAACAACATCAGTAGCTAGCGA
AAATGGTTCGTCCAATGCCAGATTGAGAAGAAGGGCTAATTTCTTTCGGAATTCACTGATAGGTCCAGAATATTCTTCAG
CTAAAATTGGAAATTCAAGAATTCCAGGCAGAATAACCATCGGTTGTCTACAGAAAGCTGATATGCGTAGAAGAGTTGTG
CCTTTGCCGGATTCCATACAAGAGCTACTTGATATCGGTGCTGAGAAATTTGGCATCTCTCTCACTGAAGTACTAACTGA
AGATGGAGCACTTATTGAGGACATTGCACTGATAAGAGATGGAGATCATCTAGTTCTTGCTACTTCAGAAAATTAA

ORF - retro_stub_19 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.92 %
Parental protein coverage: 58.3 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRAYSMDDKSSHYSITSAILPSLGAHTNCKTKLRRYIISPSNPRYRAWNAYLVLLVFYTAWASPFQFGFLD
R.YSM.D.SSHY.I.S.ILPSLG.H...K..LR.YIISP.NPRY..W.A.LVLLVFYTAWASPFQ.GFL.
RetrocopyRVYSMEDISSHYCINSGILPSLGGHSDSKIRLRNYIISPTNPRYKVWDAFLVLLVFYTAWASPFQIGFLE
ParentalRPRGVIPILDNIANSFFAIDIVLT-FFVAYLDKSACSMIDDPKRIALRYTKSGFLFDVISTIPSELIRKS
.P.G.I.ILDNI.N.FFAIDI.L..FFVAYLDKS...MIDDPKRIALRY.K.GF.FD.ISTIP.E.....
RetrocopyTPQGLIAILDNIVNFFFAIDIILSLFFVAYLDKSTYTMIDDPKRIALRYIKYGFIFDFISTIPYEAL---
ParentalTPYFLQSYEYFSILRLWRLRRVSAMFARLEKNRKISYFGVRVLKLICVTLFAVHCAGCFYYFLAARKQDT
.P..LQSY...S.LRLWRLRRVSAMF..LEKN.K.SYFG.RVLKL.CVTLFAVH.AGCFYYFLAAR..D.
Retrocopy-PRILQSYGFLSMLRLWRLRRVSAMFVELEKNNKLSYFGIRVLKLVCVTLFAVHSAGCFYYFLAARIKDV
ParentalSKTWLSLAIGNHHDRSIWDLYVMCMYWSITTLTTTGYGDLHAVATEEMIFTMFYMLFDLGLTAYLIGNMT
SKTWLSL..GN.HDRSIWDLYVM.MYWSITTLTTTGYGDLHAV.TEEMIFTM.YMLFDLGLTAYLIGNMT
RetrocopySKTWLSL--GNLHDRSIWDLYVMSMYWSITTLTTTGYGDLHAVTTEEMIFTMVYMLFDLGLTAYLIGNMT
ParentalNLVVHGTSKTRKFRDTIQAASSFAQRNKLPVRLEEQMIAHLRLRHRTDSEGLQQQETLETLPKAIRSGIS
NLVVHGT.KT.KFRD.IQAASSFAQRN.LPVRLEEQM..HL...HRTD.EGLQQQETLETLP.AIRS.IS
RetrocopyNLVVHGTNKTQKFRDAIQAASSFAQRNNLPVRLEEQMLDHLSMMHRTDTEGLQQQETLETLPRAIRSAIS
ParentalHYLFYPLVDKVYLFHGVSNDLLFQLVSEMKAEYFPPKEDVILQNEAPTDLYILVTGAVDLISHKNGMDQV
H.LFY.LVDK.YLF.G.SNDLLFQL.SEMKAEYFPPKEDVILQNEA.T.LYILVTGAVDLISHKNGMD.V
RetrocopyHHLFYSLVDKAYLFQGISNDLLFQLISEMKAEYFPPKEDVILQNEASTELYILVTGAVDLISHKNGMDHV
ParentalVGELKMGDVCGEVGVLCCRPQLFNVRTKKVSQLLRLDRSSFFNIVKTNIGDGTIIMNNLLQHLKERRDPM
VGELK.GDVCGEVG.LCCRPQLF.VRTK..SQLLRLDR.SFFN.VK.N.GD.TIIMNNLLQHLKE..DPM
RetrocopyVGELKAGDVCGEVGILCCRPQLFTVRTKRISQLLRLDRTSFFNTVKANKGDRTIIMNNLLQHLKEQTDPM
ParentalMTAILADIEHMLT
MTA.LADIEH..T
RetrocopyMTAVLADIEHIFT

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






RNA-Seq - click to see more details

Solanum tuberosum was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Solanum tuberosum was not studied using ChIP-Seq data.

EST - click to see more details

Solanum tuberosum was not studied using EST data.

TSS - click to see more details

Solanum tuberosum was not studied using FANTOM5 data.

Lab - click to see more details

retro_stub_19 was not experimentally validated.

Retrocopy orthology:
Solanum tuberosum 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Solanum tuberosum PGSC0003DMG400029083 1 retrocopy
retro_stub_19 ,




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