RetrogeneDB ID: retro_vvin_26

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 15:2868388..2869672(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_15s0024g01440
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_10s0116g00760
• Aliases: None
• Description: None

Sequence

>retro_vvin_26
ATGCTGACTTTGAATCTTGTTCCTTGTAGCAATATCACTTTATCCAAGCCAAAAAGCCATCAGTACTCTATAAATGCTCT
CCACAGGGCTCAGAACCAAGGTGACTTCCACTTGCCTAGGGGTCTGTTCAACAAGCCCAAGTCTCAGGTAATCTCAAACT
TGAGTAGAATCCATGGATACCCTTTTGGGTTTTGTGCAAAACCCAGTTCTCAGATCCATGATACAAGCGCAAAGATCAAA
TCTTTGGACACAACGGGTGAGCACCCATCTGGGGTTGGTGCAAAGCCCAGATCTTGGGTTGCTAAAGCTGCTGAGTTTGA
GGGGGAAAGTGAAGTTTCCAAGCCTAACAAGACCCTTCAACTTGGTATTGTGTTTGGGATGTGGTATTTTCAGAATATTG
TGTTCAATATCTACAACAAGAAGGTGTTGAATCTGTTCCCCTTTCCATGGCTTCTTGCCTCTTTTCAGCTATTTGTTGGG
TCTGTTTGGATGCTCATTCTCTGGTCTTTTAAGCTCCAGCCATGCCCAAAAATCTCAAAACCTTTCATTGTTGCTCTTCT
TGGGCCTGCACTGTTTCACACAATAGGCCACATCTCCGCCTGTGTTTCTTTCTCTAAGGTGGCTGTCTCGTTCACCCATG
TCATCAAATCTTCAGAACCAGTTTTCTCAGTCATTTTCTCAACCATTTTAGGTGATAACACCTACCCTTTACGTGTCTGG
CTTTCAATCCTCCCCATTGTTCTAGGTTGCTCTCTTGCCGCTGTCACCGAAGTCTCCTTCAATTTGCAAGGCCTGTGGGG
GGCTTTGATCAGCAATGTGGGGTTCGTTCTTCGCAACATTTACTCAAAGCGAAGCTTAGAGAGCTTCAAGGAAGTGAATG
GGCTGAATTTATATGGTTGGATCAGTATAATTTCATTGCTGTATCTGTTTCCTGTGGCAATTTTCGTTGAAGGGACTCAA
TGGATTGAAGGGTATCACAGAGCAATCCAAGCAGTGGGAAAACCAACCACATTTTATATATGGGTGATGTTGTCCGGGGT
GTTTTACCATCTCTACAATCAGTCATCATATCAAGCACTTGATGACATTAGCCCACTGACCTTCTCTGTTGGAAACACAA
TGAAGAGGGTGGTAGTGATTGTAGCCACTATTTTGGTGTTCAGAAATCCTGTTAAGCCTTTGAATGCGCTTGGATCTGCC
ATTGCGATTTTTGGGACTTTCTTGTATTCGCAGGCAACATCCAAGAAAAGCCCAAAGAAAATTGAAGGTGAAAAGAGTAG
TTAA

Alignment

ORF - retro_vvin_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.37 %
• Parental protein coverage: 77.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELSDQEARSEAAQKLKIGIYFATWWALNVVFNIYNKKVLNAFPYPWLTSTLSLATGSLMMLISWAVRIAE
          E.......S.....L..GI.F..W...N.VFNIYNKKVLN.FP.PWL.....L..GS..MLI.W......
Retrocopy EFEGESEVSKPNKTLQLGIVFGMWYFQNIVFNIYNKKVLNLFPFPWLLASFQLFVGSVWMLILWSFKLQP

Parental  PPKTDLDFWKTLFPVAVAHTIGHVAATVSMSKVAVSFTHIIKSGEPAFSVLVSRFLLGETFPVPVYFSLL
          .PK....F...L...A..HTIGH..A.VS.SKVAVSFTH.IKS.EP.FSV..S..L...T.P..V..S.L
Retrocopy CPKISKPFIVALLGPALFHTIGHISACVSFSKVAVSFTHVIKSSEPVFSVIFSTILGDNTYPLRVWLSIL

Parental  PIIGGCALAAVTELNFNMTGFMGAMISNLAFVFRNIFSKRGMKG-KSVGGMNYYACLSMLSLLILTPFAI
          PI..GC.LAAVTE..FN..G..GA.ISN..FV.RNI.SKR.....K.V.G.N.Y...S..SLL.L.P.AI
Retrocopy PIVLGCSLAAVTEVSFNLQGLWGALISNVGFVLRNIYSKRSLESFKEVNGLNLYGWISIISLLYLFPVAI

Parental  AVEGPQMWAAGWQKAISQIG--PNFIWWVAAQSVFYHLYNQVSYMSLDQISPLTFSIGNTMKRISVIVSS
          .VEG.Q.W..G...AI...G....F..WV....VFYHLYNQ.SY..LD.ISPLTFS.GNTMKR..VIV..
Retrocopy FVEGTQ-WIEGYHRAIQAVGKPTTFYIWVMLSGVFYHLYNQSSYQALDDISPLTFSVGNTMKRVVVIVAT

Parental  IIIFHTPVQPINALGAAIAILGTFLYSQA
          I..F..PV.P.NALG.AIAI.GTFLYSQA
Retrocopy ILVFRNPVKPLNALGSAIAIFGTFLYSQA

Legend:

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

Expression

RNA-Seq

Vitis vinifera was not studied using RNA-Seq expression data.

ChIP-Seq

Vitis vinifera was not studied using ChIP-Seq data.

EST

Vitis vinifera was not studied using EST data.

TSS

Vitis vinifera was not studied using FANTOM5 data.

Lab

retro_vvin_26 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00062p00036220	1 retrocopy	retro_atri_14,
Musa acuminata	GSMUA_Achr7G03380_001	1 retrocopy	retro_macu_2,
Physcomitrella patens	PP1S70_177V6	1 retrocopy	retro_ppat_10,
Vitis vinifera	VIT_10s0116g00760	1 retrocopy	retro_vvin_26 ,