RetrogeneDB ID: retro_vvin_20

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 14:25646582..25647572(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_14s0068g02000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_05s0020g02560
• Aliases: None
• Description: None

Sequence

>retro_vvin_20
ATGCCTTCGATTCCTGAAGAGCCCTTGCTCGCTCCTAACCCAGATCGGTTCTGTATGTTCCCGATTCAGTACCCTGAAGT
CTGGGAAATGTACAAGAAGGCCGAGGCGTCGTTTTGGACAGCCGAGGAAGTCGACCTCTCTCAGGACCAGCGTCAATGGG
AAAACCTCACCAGCGACGAGAAGCACTTCATCAGTCATATCCTTGCCTTCTTCGCCGCTTCTGACGGAATCGTCCTCGAA
AACCTCGCCGGAAGGTTCATGAAGGAGGTCCAGGTCGCCGAGGCTCGTGCCTTCTATGGATTTCAGATTGCCATTGAAAA
CATCCACTCCGAGATGTACAGTCTGTTGTTAGAATCGTATATCAAGGATCCAAAGGAGAAAAACAGGCTCTTTCACGCAA
TCGATACCATCCCCTGTGTAGCGAAGAAAGCCCAGTGGGCTCTCCGATGGATCGACGGCTCCGAAACCTTTGCCGAACGC
CTGCTCGCATTCGCCTGCGTGGAAGGCATCTTCTTCTCCGGAAGCTTCTGCTCGATATTCTGGCTAAAGAAACGCGGTCT
CATGCCGGGATTAACTTTCTCAAATGAGTTAATCTCGCGAGACGAGGGCTTACACTGCGACTTCGCGTGCTTGCTCTACA
GCCTACTTAGGAATAAACTGAGCGAGGAGAGAGTGAAGGCAATCGTCGCCGACTCGGTGGATATAGAAAGAGAGTTCGTC
TGCGACGCGTTGCCGTGCGCTCTAGTGGGGATGAACAGTGCTCTAATGAGCCAATACATCGAATTCGTTGCCGATCGCCT
GCTCGGCGCCTTGGGTTACGGGAAGATGTACAACGTTTCGAATCCGTTCGACTGGATGGAGCTAATCTCTTTACAGGGAA
AGACCAACTTCTTCGAGAAGAGGGTTGGGGAGTATCAGAAGGCTTCAGTGATGTCAAGCTTGAACGGTGACGGAGATACC
CACGTCTTCAAGATGGATGAAGATTTCTGA

Alignment

ORF - retro_vvin_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.66 %
• Parental protein coverage: 81.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEPILMKNSQRFCMFPIRYRQLWEMYKKAEASFWTAEEVDLSHDVQQWESLSNSEKHFISHVLAFFAASD
          EEP.L..N..RFCMFPI.Y...WEMYKKAEASFWTAEEVDLS.D..QWE.L...EKHFISH.LAFFAASD
Retrocopy EEPLLAPNPDRFCMFPIQYPEVWEMYKKAEASFWTAEEVDLSQDQRQWENLTSDEKHFISHILAFFAASD

Parental  GIVLENLAARFLHDIQIPEARAFYGFQIAMENIHSEMYSLLLETYIKDSKEKHRLFNAIESISCVAGKAK
          GIVLENLA.RF....Q..EARAFYGFQIA.ENIHSEMYSLLLE.YIKD.KEK.RLF.AI..I.CVA.KA.
Retrocopy GIVLENLAGRFMKEVQVAEARAFYGFQIAIENIHSEMYSLLLESYIKDPKEKNRLFHAIDTIPCVAKKAQ

Parental  WALDWIQSSTLFAERLIAFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSL
          WAL.WI..S..FAERL.AFACVEGIFFSGSFC.IFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSL
Retrocopy WALRWIDGSETFAERLLAFACVEGIFFSGSFCSIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSL

Parental  LQKQLPWQKVHHIVHEAVEIETQFVCEALPCALIGMNATLMSQYIKFVADRLLVALGYERKYNVENPFDW
          L...L....V..IV...V.IE..FVC.ALPCAL.GMN..LMSQYI.FVADRLL.ALGY...YNV.NPFDW
Retrocopy LRNKLSEERVKAIVADSVDIEREFVCDALPCALVGMNSALMSQYIEFVADRLLGALGYGKMYNVSNPFDW

Parental  MEFISLQ
          ME.ISLQ
Retrocopy MELISLQ

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_20 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00025p00110680	1 retrocopy	retro_atri_2,
Brassica rapa	Bra014962	1 retrocopy	retro_brap_7,
Prunus persica	PRUPE_ppa008063mg	1 retrocopy	retro_pper_7,
Solanum lycopersicum	Solyc01g080210.2	1 retrocopy	retro_slyc_6,
Theobroma cacao	TCM_020494	1 retrocopy	retro_tcac_4,
Vitis vinifera	VIT_05s0020g02560	1 retrocopy	retro_vvin_20 ,