RetrogeneDB ID: retro_hvul_75

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:537930126..537930615(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_37833
• Aliases: None
• Description: None

Sequence

>retro_hvul_75
CTCTTCTACCCGACGCTCGCCTACAGCATGGCCCGGAACCAACTCTCGTCGGACTACCACTGGTGGGACGCCGTCGACGG
CACCCACGTCCTGCTCGGCGCCGTGCCGTTCCCGAGCGACGTGCCGCGGCTCCACGCCCTGGGCGTCACCGCCGTCGTGA
CGCTCACCGAGCCCTACGAGCGGCTCGTGCCCACGTCGCTGTACAAGCAGCACGAGATGGAGAACCTGGTGCTGCCGACC
ACGGACTACCTCTACGCGCCGTCGCAGGACGACCTCCGCCGCGCCACGGCCTTCATCCACGGCAAGGAGGCCGGCGGCGG
GCTCACCTACGTGCACTGCAAGGCCGGCCGCGCGCGCAGCGCCACGCTGGTCATGTGCTACCTGGTGCGGTACAAGGGGA
TGACGGCGGTGGAGGCGTACGACAAGGTGCGGTCGTGCCGGCCCAGGGTGTCGCTGGCTCCGGCGCAGTGGCAGGCGGTC
CGGGACTTC

Alignment

ORF - retro_hvul_75 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.87 %
• Parental protein coverage: 54.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFYPTLVYNVVRNQCESHFHWWDQVD-EHVLLGAVPFPSDVLRLQKLGVCGVVTLNESYERLVSKSLYEA
          LFYPTL.Y...RNQ..S..HWWD.VD..HVLLGAVPFPSDV.RL..LGV..VVTL.E.YERLV..SLY..
Retrocopy LFYPTLAYSMARNQLSSDYHWWDAVDGTHVLLGAVPFPSDVPRLHALGVTAVVTLTEPYERLVPTSLYKQ

Parental  HGIENLVLPTRDYLYAPSFDNLCKAADFIHRNASCGKLTYVHCKAGRGRSTTVVLCYLVQYKQMTPAGAF
          H..ENLVLPT.DYLYAPS.D.L..A..FIH.....G.LTYVHCKAGR.RS.T.V.CYLV.YK.MT...A.
Retrocopy HEMENLVLPTTDYLYAPSQDDLRRATAFIHGKEAGGGLTYVHCKAGRARSATLVMCYLVRYKGMTAVEAY

Parental  EHVRSCRPRVLLASAQWKAVQEF
          ..VRSCRPRV.LA.AQW.AV..F
Retrocopy DKVRSCRPRVSLAPAQWQAVRDF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Hordeum vulgare was not studied using RNA-Seq expression data.

ChIP-Seq

Hordeum vulgare was not studied using ChIP-Seq data.

EST

Hordeum vulgare was not studied using EST data.

TSS

Hordeum vulgare was not studied using FANTOM5 data.

Lab

retro_hvul_75 was not experimentally validated.

Homology

Retrocopy orthology:

Hordeum vulgare 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_27787	1 retrocopy	retro_atau_4,
Hordeum vulgare	MLOC_37833	1 retrocopy	retro_hvul_75 ,