RetrogeneDB ID: retro_vvin_19

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 14:26235726..26236578(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_14s0171g00430
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_19s0085g00730
• Aliases: None
• Description: None

Sequence

>retro_vvin_19
ATGGGCAGCAGCCAAGCAGCAGTTTCCTTCCTCACGAACCTCGCCAGAGCCGCCTTTGGGCTAGGCGCCGCTGCCTCAGT
TCTGAACGCCTCTCTCTATACTGTTGACGGCGGCCAACGCGCCGTCCTCTTCGACCGTTTCCGCGGTGTGATCGACGACA
CCATCGGCGAAGGCACCCATTTCCTGGTGCCATGGCTTCAAAAGCCCTATATTTTCGATATTCGCACCCGCCCCCACACG
TTCTCCTCCGTCTCCGGCACTAAGGATCTCCAAATGGTCAACCTCACCCTCCGTGTCCTCTCTCGCCCCGAAGTCTCACG
CCTCCCCTACATTTTCAAAACCTTAGGTTTGGAGTACGACGAGAAGGTCCTTCCTTCAATCGGTAATGAGGTTCTGAAGG
CCGTCGTTGCTCAATTCAACGCGGATCAGCTTCTCACGGACCGGCCACATGTGTCGGCTCTCGTCCGCGACAGCTTGATT
CGCCGGGCCAAGGACTTCAATATTGTTCTGGATGACGTCGCTATTACGCATTTGAGCTACGGGGCGGAGTTCTCCAAGGC
TGTGGAGCAGAAGCAGGTGGCGCAGCAGGAGGCGGAGCGCTCCAAGTTTGTAGTGGCCAAGGCGGAGCAGGAACGTAGGG
CCGCAATTATTCGGGCAGAGGGTGAGAGCGAGTCTGCCAAGCTCATCTCGGATGCCACTGCTGCTGCAGGAATGGGGTTG
ATTGAGCTTAGGAGGATTGAGGCTTCAAGGGAGATTGCAGCTACTCTGGCGAAAACACCCAATGTGGCTTACTTGCCTGG
TGGGAATAACATGCTTTTGGGGCTGAACCCTACTATTGCGGGAGGGCGTTGA

Alignment

ORF - retro_vvin_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.33 %
• Parental protein coverage: 71.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLYNVEGGHRAIVFNRIVGVKDKVYPEGTHLMIPWFDRPVIYDVRTRPHLVESTSGSHDLQMVKIGLRVL
          SLY.V.GG.RA..F.R..GV.D....EGTH...PW...P.I.D.RTRPH...S.SG..DLQMV...LRVL
Retrocopy SLYTVDGGQRAVLFDRFRGVIDDTIGEGTHFLVPWLQKPYIFDIRTRPHTFSSVSGTKDLQMVNLTLRVL

Parental  TRPLPDQLPTIYRTLGENYNERVLPSIIHETLKAVVAQYNASQLITQRETVSREIRKLLTERAANFNIAL
          .RP....LP.I..TLG..Y.E.VLPSI..E.LKAVVAQ.NA.QL.T.R..VS...R..L..RA..FNI.L
Retrocopy SRPEVSRLPYIFKTLGLEYDEKVLPSIGNEVLKAVVAQFNADQLLTDRPHVSALVRDSLIRRAKDFNIVL

Parental  DDVSITSLTFGREFTAAIEAKQVAAQEAERAKFVVEKAEQDKRSAIIRAQGEAKSAQLIGQA-IANNPAF
          DDV.IT.L..G.EF..A.E.KQVA.QEAER.KFVV.KAEQ..R.AIIRA.GE..SA.LI..A..A.....
Retrocopy DDVAITHLSYGAEFSKAVEQKQVAQQEAERSKFVVAKAEQERRAAIIRAEGESESAKLISDATAAAGMGL

Parental  ITLRKIEASREIAHTISNSANKVFL-NSNDLLLNL
          I.LR.IEASREIA.T.....N...L...N..LL.L
Retrocopy IELRRIEASREIAATLAKTPNVAYLPGGNNMLLGL

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_19 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
Oryza meridionalis	OMERI03G37300	1 retrocopy	retro_omer_25,
Prunus persica	PRUPE_ppa009505mg	1 retrocopy	retro_pper_51,
Vitis vinifera	VIT_19s0085g00730	1 retrocopy	retro_vvin_19 ,