RetrogeneDB ID:

retro_stub_4

Retrocopy
location
Organism:Potato (Solanum tuberosum)
Coordinates:4:45573797..45574844(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:PGSC0003DMG403023117
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:PGSC0003DMG400001375
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_stub_4
ATGTCTCAAGTCAGCGTCAGAGATGATGAGGTAGATATTGTGATAGCTGCAATTGAACCAGATCTTACTTCTTTTCTGGA
AGAATGGAGAGCAATATTCTCCCGATTTCACCTGATTATTATCAAAGATCCTGACGTCAAAGGAGAACTTAAAATTCCAG
GTGGATTTAATTATGATACCTATACAAAAGCTGATATTCAACAAATTATTGGACCTTCAAATGCTGCAACTTTCTCTGGC
TACTCGTGCCGATATTTTGGCTATCTCTTGTCAAAGAAGAAATATATCATCTCAATTGATGATGACTGCATTCCAGCTAA
GGATACTAAGGGTATCCAAGTCGATGCCATCGCACAACATATCAATAACCTCTTGACTCCTGCCACCCCATTTTTCTTTA
ATACCCTCTATGATCCTTTCTGTAAAGGAGCTGATTTTGTTCGTGGCTACCCATTTAGCTTGCGAAGTGGTGTCTCGTGT
GCTCTATCATGTGGACTGTGGCTTAATTTAGCAGATCTTGATGCACCTACACAAGCCCTCAAGCCGGAGCTGAGAAACAC
TCGATATGTTGATGCTGTCCTCACTGTACCAGCTAGGGCCATGATGCCTCTGAGCGGAATCAATATAGCGTTTGATCGCG
AATTGGTGGGACCTGCTTTGCTGCCATCTTTCAAGTTGGCAAAGGAAGGAAAGTTCAGGTGGGAAACTGTGGAGGATGTA
TGGACTGGAATGTGTGTTAAGGTAGTATGTGATCACTTAGGATATGGTTTGAAAACTGGGCTTCCATATGTGTGGAGGAA
AGAAAGAGGTGATGCCATAGAGAGTTTGAAGAAAGAGTGGGAAGGGGTGAAGCTGATGGAAGAAGTTGTTCCATTCTTCC
AATCAATGAAATTGACCCCGGCAGCAAAAACAGCTGAAGATTGTGTGATTGAGATTGCAGCAGCCGTGAAGGAGCAGCTG
GGACGAATAGATCCTGTGTTCACCCGTGCAGCTGATTCCATGGTCGAGTGGGTGCAGCTGTGGAAGACTGTCAAAACCCG
AACATAA

ORF - retro_stub_4 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.75 %
Parental protein coverage: 59.44 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDELDIVIPTIRN--LDFLEMWRPFFEQYHLIIVQDGDPSKTIKVPDGFDYELYNRNDINKILGPRASCIS
DE.DIVI..I......FLE.WR..F...HLII..D.D.....K.P.GF.Y..Y...DI..I.GP......
RetrocopyDEVDIVIAAIEPDLTSFLEEWRAIFSRFHLIIIKDPDVKGELKIPGGFNYDTYTKADIQQIIGP-SNAAT
ParentalFKDSACRCFGYMVSKKKYIFTIDDDCFVAKDPSGKDINALEQHIKNLLCPSTPYFFNTLYDPFRDGADFV
F....CR.FGY..SKKKYI..IDDDC..AKD..G....A..QHI.NLL.P.TP.FFNTLYDPF..GADFV
RetrocopyFSGYSCRYFGYLLSKKKYIISIDDDCIPAKDTKGIQVDAIAQHINNLLTPATPFFFNTLYDPFCKGADFV
ParentalRGYPFSLREGVSTAVSHGLWLNIPDYDAPTQLVKPLERNTRYVDTVLTIPKGTLFPMCGMNLAFDRDLIG
RGYPFSLR.GVS.A.S.GLWLN..D.DAPTQ..KP..RNTRYVD.VLT.P.....P..G.N.AFDR.L.G
RetrocopyRGYPFSLRSGVSCALSCGLWLNLADLDAPTQALKPELRNTRYVDAVLTVPARAMMPLSGINIAFDRELVG
ParentalPAM
PA.
RetrocopyPAL

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






Solanum tuberosum was not studied using RNA-Seq expression data.
Solanum tuberosum was not studied using ChIP-Seq data.
Solanum tuberosum was not studied using EST data.
Solanum tuberosum was not studied using FANTOM5 data.
retro_stub_4 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 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Solanum tuberosum PGSC0003DMG400001375 1 retrocopy
retro_stub_4 ,
Solanum lycopersicum Solyc02g089170.21 retrocopy
Vitis vinifera VIT_14s0083g011001 retrocopy



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