RetrogeneDB ID: retro_vvin_27

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 4:16084210..16085284(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_04s0023g00110
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_14s0083g01100
• Aliases: None
• Description: None

Sequence

>retro_vvin_27
ATGTCTCAAACAAACATTGGTGACGATGAGGTTGACATTGTGATTGGTGCACTCCATGCTGACCTCACATCCTTCCTGAA
TGAATGGAGACCACTATTCTCCCGATTTCACCTGATAATCGTGAAAGACCCTGACCTCAGAGAGGAGCTCAAAATACCAG
AAGGCTTTAACCTCCACGTCTATACCAAGTCCGACATTGACCGAGTGGTGGGCTCGTCTTACACTGCCATTAATTTCTCT
GGTTACTCATGTCGGTACTTTGGCTATCTCATGTCTAGGAAAAAGTACATCTTCTCAGTCGATGATGACTGCATCCCAGC
AAAGGACGATAAGGGTCTTTCAGTAGATGCGGTCGACCAGCATATCACCAACCTTGCGACTCCAGCCACCCCTTTCTTCT
TTAACACACTGTACGACCCTTTCCGCAAAGGAACAGATTTTGTTCGTGGGTACCCATTTAGCTTGCGGAGTGGAGTAACA
TGTGCTCTGTCATGTGGGCTCTGGCTGAACTTAGCTGACCACGATGCGCCCACACAAGCCCTCAAGCCAGGGCATAGGAA
TTCTCGGTATGTTGACGCTGTTCTGACTGTTCCAGCCAGAGCTCTGATGCCTGTGAGCGGTGTGAACATTGCTTTCAACC
GGGAGCTGGCTGGACCAGCCTTGTTCCCAGGTCTGAGGCTGGCAGCTGAAGGAAAGCTGAGGTGGGAAACAGTGGAAGAC
ATATGGTGCGGACTCTGTGTGAAGGTGGTATGCGATCACCTTGGGCTTGGTGTGAAAACCGGGCTGCCATATGTGTGGAG
AAACGACAGAGGCAATGCCATAGAAAGCTTGAAGAAAGAGTGGGAAGGCGTGAAGCTGATGGAGGAAGTCGTCCCGTTCT
TTCAGTCTGTGAGGTTGTCACAAGCAGCAGTCACAACAGAGGACTGCATGCTGGAGATAGTGGCATTGGTGAAGGAGCGG
CTGGCAACATTGGATCCGGTCTTCGCTCGTGCTGCCCAAGCCATGGCCGATTGGATCAAGCTCTGGAAGGCAGTTGGATC
AGGATCAGGATCCTCGCGGCCTTCTAATGGGTAA

Alignment

ORF - retro_vvin_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.14 %
• Parental protein coverage: 95.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DELDIVIPTIRN--LDFLEMWRPFFQPYHLIIVQDGDPSKTIKVPDGFDYELYNRNDINKILGPKASCIS
          DE.DIVI.........FL..WRP.F...HLIIV.D.D.....K.P.GF....Y...DI....G.....I.
Retrocopy DEVDIVIGALHADLTSFLNEWRPLFSRFHLIIVKDPDLREELKIPEGFNLHVYTKSDIDRVVGSSYTAIN

Parental  FKDSACRCFGYMVSKKKYIFTIDDDCFVAKDPSGKQINALEQHIKNLLSPSTPFFFNTLYDPFREGADYV
          F....CR.FGY..S.KKYIF..DDDC..AKD..G....A..QHI.NL..P.TPFFFNTLYDPFR.G.D.V
Retrocopy FSGYSCRYFGYLMSRKKYIFSVDDDCIPAKDDKGLSVDAVDQHITNLATPATPFFFNTLYDPFRKGTDFV

Parental  RGYPFSLREGVPTAVSHGLWLNIPDYDAPTQLVKPLERNTRFVDAVLTIPKGTLFPMCGMNLAFDRDLIG
          RGYPFSLR.GV..A.S.GLWLN..D.DAPTQ..KP..RN.R.VDAVLT.P...L.P..G.N.AF.R.L.G
Retrocopy RGYPFSLRSGVTCALSCGLWLNLADHDAPTQALKPGHRNSRYVDAVLTVPARALMPVSGVNIAFNRELAG

Parental  PAMYFGLMGDGQPIGRYDDMWAGWC---VKVTCDHLGLGVKTGLPYIWHSKASNPFVNLKKEYNGIFWQE
          PA...GL........R.......WC...VKV.CDHLGLGVKTGLPY.W.....N....LKKE..G....E
Retrocopy PALFPGLRLAAEGKLRWETVEDIWCGLCVKVVCDHLGLGVKTGLPYVWRNDRGNAIESLKKEWEGVKLME

Parental  EIIPFFQSVSLPKDCTTVQKCYVELAKLVKEKLGKVDPYFVKLGDAMVTWIEAWDELNPAGGSAKRPNG
          E..PFFQSV.L.....T...C..E...LVKE.L...DP.F.....AM..WI..W.......GS....NG
Retrocopy EVVPFFQSVRLSQAAVTTEDCMLEIVALVKERLATLDPVFARAAQAMADWIKLWKAVGSGSGSSRPSNG

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_27 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400001375	1 retrocopy	retro_stub_4,
Solanum lycopersicum	Solyc02g089170.2	1 retrocopy	retro_slyc_3,
Vitis vinifera	VIT_14s0083g01100	1 retrocopy	retro_vvin_27 ,