RetrogeneDB ID: | retro_stub_56 | ||
Retrocopy location | Organism: | Potato (Solanum tuberosum) | |
| Coordinates: | 5:46491440..46492847(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | PGSC0003DMG400016801 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | PGSC0003DMG400011771 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_stub_56
ATGACAGATCATGTTTCTGTTACTGTGTATGATGAATCGAGTTCTTTTGATGACGATGGTCGTTTGAAAAGAAGAGGGAA
TGTTTGGACTGCAAGTGCTCATATAATTACTGCTGTGATTGATTCTGGAGTTTTAATAGTTGCTTGGGCTACTGCACAGC
TTGGATGGATTGCTGGTCCAGTTATATTGCTTCTCTTCTCCATTGTTACTTACTACACTTCTAATTTGCTCTCTGATTGT
TATCGTAAAGGTGATCAACTTACTGGGAAAAGAAACTATACGTATATGGATGCTGTTCGAGCCAATCTAGGTGGTGTTCA
TGTTAAGATTTGTGGGATACTTCAATATGCAAATATTGTTGGAGTCGCGGTTGGGTATACTATCGCGTCTTCTATTAGTA
TGGTAGCTGTGAAAAGGTCAAATTGTTTCCATGAATACGGTCATCAGGCTGCTTGTAATGTTTCAACAACTCCATACATG
ATCGCGTTTGGAGTGGTGCAGATTGTCTTGTCACAAATCCCAGATTTTGATCAGATTTCGTGGCTTTCTATTGTGGCTGC
TGTTATGTCTATGACATACTCAACGATTGGTCTTGGTTTGGGAGTTGCTAAAGTTGCTGAAACAGGGAAAGTACAAGGAA
GTTTAACTGGGGTTAGTGGTGGAACTGGAATGCAGAAGATTTGGAAAAGCTCTCAAGCTGTTGGAGCTATAGCTTTCGCG
TATTCTTACTCTCTCATACTTATTGAGATTCAGGATACAATCAAATCACCACCATCAGAAGCTAAGACGATGAAGAAGGC
ATCGTTGATAAGTGTGACAGTAACAACTGTTTTCTTCATACTCTGTGGTTGCTTTGGTTATGCAGCATTTGGAGATCAAT
CCCCTGGAAGTTTACTAACTGGATTTGGATTCTACGATCCTTATTGGCTTCTCAACATCGCAAACATGGCTGTCGTTGTA
CACCTAGTGGGTGCTTACCAAGTTTACTGCCAACCCCTTTTCGCCTATGTTGAAAAAACAGCAGCTGAACGGTACCCTGA
CAGTATAATCATCATGAAGGAGATTGATATTCCGATCCCTGGCTGTAAGCCCTTCAAGCTCAACTTTTTCCGTCTAGTAT
GGAGGACAGTTTTCGTGATCTTCACAGTTCTCATTTCTATGTTGATGCCATTCTTTAACGATATTGTTGGCATTCTTGGA
GCCTTTGGATTTTGGCCACTTACAGTCTACTTCCCAGTAAAAATGTACATTGTGGAAAAGAATATTACCAAATGGAGTGG
AAGATGGATCTGCCTTCAACTACTTAGTGGTGCTTGCCTTGTTATCTCGATTGCTGCAGCTGCTGGTTCTTTTGCTGGAC
TTGTTTCTGATTTACAAGTTTCCTGGCCTTTCAAGACGCTTAATTAA
ORF - retro_stub_56 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.12 % |
| Parental protein coverage: | 98.52 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | HQVFEVYGESKCFDDDGRIKRTGSVWTASAHIITAVIGSGVLSLAWATAQLGWVAGPTVLLLFSFVTYYT |
| H....VY.ES..FDDDGR.KR.G.VWTASAHIITAVI.SGVL..AWATAQLGW.AGP..LLLFS.VTYYT | |
| Retrocopy | HVSVTVYDESSSFDDDGRLKRRGNVWTASAHIITAVIDSGVLIVAWATAQLGWIAGPVILLLFSIVTYYT |
| Parental | SALLSDCYRTGDPVTGKRNYTYMDAVRANLGGFQVKICGVIQYANLFGVAIGYTIAASISMVAVNRSNCF |
| S.LLSDCYR.GD..TGKRNYTYMDAVRANLGG..VKICG..QYAN..GVA.GYTIA.SISMVAV.RSNCF | |
| Retrocopy | SNLLSDCYRKGDQLTGKRNYTYMDAVRANLGGVHVKICGILQYANIVGVAVGYTIASSISMVAVKRSNCF |
| Parental | HKQGHRAACNVSSTPYMIIFGVMEIIFSQIPDFDQISWLSIVAAVMSFTYSTIGLGLGVAQVAETGKIEG |
| H..GH.AACNVS.TPYMI.FGV..I..SQIPDFDQISWLSIVAAVMS.TYSTIGLGLGVA.VAETGK..G | |
| Retrocopy | HEYGHQAACNVSTTPYMIAFGVVQIVLSQIPDFDQISWLSIVAAVMSMTYSTIGLGLGVAKVAETGKVQG |
| Parental | SLTGISIGTEVTEMQKIWRSFQALGAIAFAYSYSLILIEIQDTLKSPPAEAKTMKRATLISVAVTTVFYM |
| SLTG.S.G...T.MQKIW.S.QA.GAIAFAYSYSLILIEIQDT.KSPP.EAKTMK.A.LISV.VTTVF.. | |
| Retrocopy | SLTGVSGG---TGMQKIWKSSQAVGAIAFAYSYSLILIEIQDTIKSPPSEAKTMKKASLISVTVTTVFFI |
| Parental | LCGCFGYAAFGDQSPGNLLTGFGFYNPYWLLDIANVAIVVHLVGAYQVYCQPLFAFVEKTATEWYPDSKI |
| LCGCFGYAAFGDQSPG.LLTGFGFY.PYWLL.IAN.A.VVHLVGAYQVYCQPLFA.VEKTA.E.YPDS.I | |
| Retrocopy | LCGCFGYAAFGDQSPGSLLTGFGFYDPYWLLNIANMAVVVHLVGAYQVYCQPLFAYVEKTAAERYPDSII |
| Parental | ITKEIDVPIPGFKPFKLNLFRLVWRTIFVIITTVISMLMPFFNDVVGILGAFGFWPLTVYFPVEMYIVQK |
| I.KEID.PIPG.KPFKLN.FRLVWRT.FVI.T..ISMLMPFFND.VGILGAFGFWPLTVYFPV.MYIV.K | |
| Retrocopy | IMKEIDIPIPGCKPFKLNFFRLVWRTVFVIFTVLISMLMPFFNDIVGILGAFGFWPLTVYFPVKMYIVEK |
| Parental | RITKWSGRWICLQILSGACLVISIAAAAGSFAGVASDLKVYRPFQS |
| .ITKWSGRWICLQ.LSGACLVISIAAAAGSFAG..SDL.V..PF.. | |
| Retrocopy | NITKWSGRWICLQLLSGACLVISIAAAAGSFAGLVSDLQVSWPFKT |
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_56 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Solanum tuberosum | PGSC0003DMG400011771 | 2 retrocopies |
retro_stub_25, retro_stub_56 ,
|