RetrogeneDB ID: retro_vvin_15

Retrocopy location

• Organism: Grape (Vitis vinifera)
• Coordinates: 18:412258..413077(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: VIT_18s0122g00480
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: VIT_08s0007g03950
• Aliases: None
• Description: None

Sequence

>retro_vvin_15
ATGGCGGAGCACTTGGCTTCCATCTTCGGCACCGAAAAGGACCGCGTGAACTGTCCGTTTTATTTCAAGATCGGTGCTTG
TCGTCACGGAGATCGATGCTCGCGCCTCCACAATCGCCCCACGATCTCCCCAACGCTTCTCCTCTCCAACATGTATCAGC
GTCCCGACATGATTACTCCAGGTGTAGACGCTCAAGGCCAGCCTATTGATCCCAGGAAGATTCAGGAACACTTTGAGGAC
TTCTACGAGGATATCTTTGAAGAGCTCGGCAAGTTCGGCGAGATCGAGAGTCTCAATGTTTGTGATAACCTGGCCGATCA
CATGATCGGTAATGTTTATGTTCAGTTCAAGGAGGAGGAGCAGGCGGCCGCTGCTTTGCAAGCTTTGCAGGGGCGGTTCT
ACTCCGGCCGCCCTATCATTGCGGATTTTTCTCCCGTTACCGACTTTCGTGAAGCAACGTGTCGCCAATTTGAGGAGAAC
AATTGCAACCGAGGGGGTTACTGTAACTTTATGCATGTGAAGCTTATTGGAAGGGATTTGAGGAGGAAGCTATTTGGGAG
GTACAGCGGATATGGGAGAAGTCGAAGCCGGAGCAGGAGTTTGAGTCCACGTTACCGGAGGGATTCTGATAGGCGAAGGA
GCGGGGACCGTGGAGATTACCGAGGAAATGGGCGACGGAGCGGGGATAAGCACGGGAGTGATGGGGGTCGAAGAAGACAT
GGCAGTCCCAGGCGGAGCAGGAGTCCGGTGAGAGAAGGGAGTGAGGAGCGCAGAGCGAGGATTGAGCTGTGGAATCGAGA
AAGAGAGGAAAGGCAGTGA

Alignment

ORF - retro_vvin_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.48 %
• Parental protein coverage: 60.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEHLASIFGTEKDRVNCPFYFKIGACRHGDRCSRLHTKPSISPTLLLSNMYQRPDMVTPGVDPQGQPLD
          MAEHLASIFGTEKDRVNCPFYFKIGACRHGDRCSRLH..P.ISPTLLLSNMYQRPDM.TPGVD.QGQP.D
Retrocopy MAEHLASIFGTEKDRVNCPFYFKIGACRHGDRCSRLHNRPTISPTLLLSNMYQRPDMITPGVDAQGQPID

Parental  PRKIQEHFEDFYEDLFEELSKYGEIESLNICDNLADHMVGNVYVQFREEEHAANALRNLNGRFYAGRPII
          PRKIQEHFEDFYED.FEEL.K.GEIESLN.CDNLADHM.GNVYVQF.EEE.AA.AL..L.GRFY.GRPII
Retrocopy PRKIQEHFEDFYEDIFEELGKFGEIESLNVCDNLADHMIGNVYVQFKEEEQAAAALQALQGRFYSGRPII

Parental  VDFSPVTDFREATCRQYEENICNRGGYCNFMHLKKISRQLRRQLFGRNR---RRRSRSRSRSPYRHRGHE
          .DFSPVTDFREATCRQ.EEN.CNRGGYCNFMH.K.I.R.LRR.LFGR.....R.RSRSRS.SP...R...
Retrocopy ADFSPVTDFREATCRQFEENNCNRGGYCNFMHVKLIGRDLRRKLFGRYSGYGRSRSRSRSLSPRYRRDSD

Parental  EHPHGPHGPHGPHGPHG--PRGPRGSNRR
          ....G..G.....G.......G..G..RR
Retrocopy RRRSGDRGDYRGNGRRSGDKHGSDGGRRR

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_15 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00040p00218420	1 retrocopy	retro_atri_1,
Theobroma cacao	TCM_041518	1 retrocopy	retro_tcac_16,
Vitis vinifera	VIT_08s0007g03950	1 retrocopy	retro_vvin_15 ,