RetrogeneDB ID: | retro_vvin_48 | ||
Retrocopy location | Organism: | Grape (Vitis vinifera) | |
| Coordinates: | 10:18011916..18012822(+) | ||
| Located in intron of: | VIT_10s0071g01150 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | VIT_04s0023g03360 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_vvin_48
ATGGAGACTCAATCATCTGCAAGAAGAGTCACAAGGTTACAAACCTTGGCTGCTTCAAACAAATTTCCCATCTCAAAGAA
ATTTGAAGAATCTGATGAGGGTGTGAAATCAAGAAAAAGACGTGAGAAGCAACAAGAACGGTCTACGCTCATTGATGTAA
CGAATGATTCTCCCATTGTTGGACTTTCAATGGGAAGCTTGGAAACCCCAGTGTCATCCATCGCAAAGAAAAAGAGAAAT
CAAGCCAAGATGACCCCTCAGTCTGGGGAGGCATTGCTTAGGGGTCAGGTGAAGACCCTATTGCAGAAGGTCGAAAAAGG
GCCGGGCTTTTGAGACTCTCATTGGAAGACTGCCCCTTTCTTCATGTTCAAGGTCTCATCAATTGCCCTATGCTTCTTGC
CCCAACTCCAACAAACACACCCCAAGTCTTGAATCTTACAGTGGAGCAAAGTATCAACAATAGCAGCATGACTTTGGTGA
TGCCTTCTCCAATGGGCCAAGAACTAAAGATCTCCAAGGTGGCCAGTAATATTTTTGACAGGGAGAAGAAAAAGAATATT
GAATTGGAAACAAGTCCAGTAACTCACCCTCTACTGTTGGATTTCTCTGAAAAATCAGAAATTGCAGAGTGCAAAGAGAA
GACACCCCATGAGGACAATGATGCTTCAGTTTGGTCTATTCAGGTTAATGCAAATATCAAGGACGAAGATGAATAAGAGG
CAGTCGAAGAAGAAGAAGAAGATTATCATGAAGAAATCAACTGAGGAAGAAAAATATGAAAATGATGGAGGAATTGTTGA
TGAACCGTGCGAAGGAATGAGCAAGATCAGCATGAATGAGAATAGAATACACAAGTTTAGAGGAAAGCACACCCAATTTG
TGTACAACACTGATGACAATCTTGTT
ORF - retro_vvin_48 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.61 % |
| Parental protein coverage: | 90.83 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | METPSSTRRVTRSQALAASNSNIPISKKFEESDKGVKSRKRSGKQQERYALVDVTNDSPIVGVAMGSLET |
| MET.SS.RRVTR.Q.LAASN...PISKKFEESD.GVKSRKR..KQQER..L.DVTNDSPIVG..MGSLET | |
| Retrocopy | METQSSARRVTRLQTLAASNK-FPISKKFEESDEGVKSRKRREKQQERSTLIDVTNDSPIVGLSMGSLET |
| Parental | PLSSMAKNKSNQSKMTPGSGEALLRGQVKTLLQKVE-EEAEHSKLSLEGRPILHVQGLISSPMLLAPTPA |
| P.SS.AK.K.NQ.KMTP.SGEALLRGQVKTLLQKVE...A....LSLE..P.LHVQGLI..PMLLAPTP. | |
| Retrocopy | PVSSIAKKKRNQAKMTPQSGEALLRGQVKTLLQKVE<KRAGLLRLSLEDCPFLHVQGLINCPMLLAPTPT |
| Parental | NTPQLLNLSVEQIINNSG---VMPSPMGQELMISEVVTDIFDGKKKENIESEASPVTRSLLSDFSEKSEI |
| NTPQ.LNL.VEQ.INNS....VMPSPMGQEL.IS.V...IFD..KK.NIE.E.SPVT..LL.DFSEKSEI | |
| Retrocopy | NTPQVLNLTVEQSINNSSMTLVMPSPMGQELKISKVASNIFDREKKKNIELETSPVTHPLLLDFSEKSEI |
| Parental | SESSECKKKTFQEDDDASVWSIQVNASIKDEDEEEA-FEEEEDYREEIE-YEEEEEEEYEENGGIVDELC |
| .E...CK.KT..ED.DASVWSIQVNA.IKDEDE.EA.......Y.EEI...EE..E......GGIVDE.C | |
| Retrocopy | AE---CKEKTPHEDNDASVWSIQVNANIKDEDE*EAVXXXXXXYHEEIN>EEEKYEND----GGIVDEPC |
| Parental | EGMSKISVNENGIAAKSRGKHTRFVYNSDDELV |
| EGMSKIS.NEN.I..K.RGKHT.FVYN.DD.LV | |
| Retrocopy | EGMSKISMNENRI-HKFRGKHTQFVYNTDDNLV |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Vitis vinifera was not studied using RNA-Seq expression data.
Vitis vinifera was not studied using ChIP-Seq data.
Vitis vinifera was not studied using EST data.
Vitis vinifera was not studied using FANTOM5 data.
retro_vvin_48 was not experimentally validated.
Retrocopy orthology:
Vitis vinifera 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 | |
|---|---|---|---|
| Vitis vinifera | VIT_04s0023g03360 | 1 retrocopy |
retro_vvin_48 ,
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