RetrogeneDB ID: retro_vvin_28

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 18:5617416..5618736(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_18s0001g07340
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_13s0084g00820
• Aliases: None
• Description: None

Sequence

>retro_vvin_28
ATGGATATCTTCACTGCATTTGTCTTCCTCACTCTTGTGGTTTCAACCACCAAAGCTTTTGATCCCTGTGCTTCCCCTTC
TTCGGAATCCAAGGGCTCGGATCTTTCGGTGATCCATGTGTATGGCCAATGCTCTCCCTTCAACCAGCACAAGGCTGGGT
CCTGGGTGAACACCGTCATCAACATGGCCTCAAAAGACCCAGCACGCGTCACCTACTTGTCCAGCCTAGTTGCATCCCCC
AAGGCCACCTCTGTCCCAATTGCGTCTGGGCAACAGGTCCTCAACATTGGCAACTACGTGGTGCGAGTCAAACTGGGCAC
TCCCGGTCAGCTTATGTTCATGGTTCTTGACACCAGCAGAGACGCCGCATGGGTCCCATGCGCCGACTGCGCCGGCTGCT
CCTCCCCCACCTTCTCCCCCAACACTTCTTCCACTTACGCTTCACTCCAATGCTCTGTGCCCCAGTGCACCCAGGTCCGT
GGCCTCTCGTGCCCCACCACGGGTACTGCTGCATGCTTCTTCAACCAAACCTATGGGGGAGATTCCTCCTTCTCCGCCAT
GCTCTCACAGGATTCTCTCGGCTTGGCGGTTGACACTCTTCCCAGCTACTCTTTCGGCTGCGTCAACGCTGTCTCCGGCT
CGACCCTTCCGCCGCAGGGGCTCCTGGGGCTGGGTCGTGGGCCCATGTCGTTGCTCTCACAATCCGGGTCTCTATACTCT
GGTGTCTTCTCCTACTGTTTTCCCAGTTTCAAATCATACTACTTCTCTGGCTCCTTACGCCTCGGACCCCTGGGTCAACC
CAAGAACATCAGAACCACCCCACTCCTCCGAAACCCGCACCGACCCACTCTCTACTACGTCAACCTAACCGGAGTCAGCG
TCGGCCGAGTTTTGGTGCCGGTGGCGCCAGAGCTACTGGCATTTGACCCAAACACCGGCGCCGGTACCATAATTGACTCA
GGTACAGTCATAACTCGGTTCGTGGAACCAGTATACGCGGCCATCAGGGACGAATTCAGGAAGCAGGTGAAAGGACCATT
TGCAACGATAGGGGCATTCGATACGTGTTTCGCAGCAACAAATGAGGACATAGCACCCCCGGTAACGTTCCATTTCACAG
GAATGGACCTGAAGTTGCCGCTGGAGAACACACTGATACACAGCAGCGCAGGGTCGTTGGCATGCTTGGCAATGGCAGCA
GCGCCCAACAACGTCAACTCGGTGCTGAACGTTATAGCGAATCTACAGCAGCAGAATCTTAGGATTATGTTTGATGTCAC
CAACTCTCGTCTGGGAATTGCTCGTGAGCTGTGTAACTAG

Alignment

ORF - retro_vvin_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.02 %
• Parental protein coverage: 96.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFLSLALGLTQP--NCETPD---QGSTLQVLHVYSPCSPFRPKEPLSWEESVLQMQAKDKARLQFLSSLV
          .FL.L....T.....C..P.....GS.L.V.HVY..CSPF......SW...V..M..KD.AR...LSSLV
Retrocopy VFLTLVVSTTKAFDPCASPSSESKGSDLSVIHVYGQCSPFNQHKAGSWVNTVINMASKDPARVTYLSSLV

Parental  A--RKSVVPIASGRQIVQNPTYIVRAKIGTPAQTMLMAMDTSSDVAWIPCNGCLGCSSTLFNSPASTTYK
          A......VPIASG.Q......Y.VR.K.GTP.Q.M.M..DTS.D.AW.PC..C.GCSS..F....S.TY.
Retrocopy ASPKATSVPIASGQQVLNIGNYVVRVKLGTPGQLMFMVLDTSRDAAWVPCADCAGCSSPTFSPNTSSTYA

Parental  SLGCQAAQCKQ---VPKPTCGGGVCSFNLTYGG-SSLAANLSQDTITLATDAVPGYSFGCIQKATGGSLP
          SL.C...QC.Q......PT.G...C.FN.TYGG.SS..A.LSQD...LA.D..P.YSFGC.....G..LP
Retrocopy SLQCSVPQCTQVRGLSCPTTGTAACFFNQTYGGDSSFSAMLSQDSLGLAVDTLPSYSFGCVNAVSGSTLP

Parental  AQGLLGLGRGPLSLLSQTQNLYQSTFSYCLPSFKSLNFSGSLRLGPVGQPKRIKYTPLLKNPRRPSLYFV
          .QGLLGLGRGP.SLLSQ...LY...FSYC.PSFKS..FSGSLRLGP.GQPK.I..TPLL.NP.RP.LY.V
Retrocopy PQGLLGLGRGPMSLLSQSGSLYSGVFSYCFPSFKSYYFSGSLRLGPLGQPKNIRTTPLLRNPHRPTLYYV

Parental  NLMAVRVGRRVVDVPPGSFTFNPSTGAGTIFDSGTVFTRLVTPAYIAVRDAFRNRV-GRNLTVTSLGGFD
          NL..V.VGR..V.V.P....F.P.TGAGTI.DSGTV.TR.V.P.Y.A.RD.FR..V.G...T........
Retrocopy NLTGVSVGRVLVPVAPELLAFDPNTGAGTIIDSGTVITRFVEPVYAAIRDEFRKQVKGPFATIGAFDTCF

Parental  TCYTVPIAAPTITFMFTGMNVTLPPDNLLIHSTAGSTTCLAMAAAPDNVNSVLNVIANLQQQNHRLLYDV
          ......IA.P..TF.FTGM...LP..N.LIHS.AGS..CLAMAAAP.NVNSVLNVIANLQQQN.R...DV
Retrocopy AATNEDIAPP-VTFHFTGMDLKLPLENTLIHSSAGSLACLAMAAAPNNVNSVLNVIANLQQQNLRIMFDV

Parental  PNSRLGVARELC
          .NSRLG.ARELC
Retrocopy TNSRLGIARELC

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_28 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo8g083640	1 retrocopy	retro_bole_10,
Brassica rapa	Bra014819	1 retrocopy	retro_brap_21,
Medicago truncatula	MTR_8g039540	1 retrocopy	retro_mtru_20,
Populus trichocarpa	POPTR_0001s06560	1 retrocopy	retro_ptri_13,
Prunus persica	PRUPE_ppa005966mg	1 retrocopy	retro_pper_11,
Theobroma cacao	TCM_045111	1 retrocopy	retro_tcac_5,
Vitis vinifera	VIT_13s0084g00820	1 retrocopy	retro_vvin_28 ,