RetrogeneDB ID: retro_hvul_78

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:81286222..81286699(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_34672
• Aliases: None
• Description: None

Sequence

>retro_hvul_78
GTCCTGTGTCCTCTTTACTACTACTACCAGCGGCACCCGGTGAACCTGCTGCTGCTGGCGCTCTTCACAGTGGCCATCAG
CTTCGCGGTGGGGTTCACCTGCGTCTTCACCAAGGGGGAGGTGATCTTGGAGTCGGCCATCCTGACGACGGTGGTGGTGG
TGAGCCTGACGGCGTACACCTTCTGGGCGGCGAGCCACGGGCACAACTTCAACTTCCTGGGCCCGTTCCTGTTCGTGGCA
GTGATGATCCTCATGGTATTCACGCTCAGCCAGGCATTCTTCCCGCTGGGCCGCATCTCGCTCATGGTGTACAGCTGGCT
GGCGGCGCTCGTCTTCTACGGCTACATCATCTACGACACCGACAACCTCATCAAGCGCTACTCCTACGACGAGTACGTCT
GGGCCGCCGTCGCGCTCTACCTCGATGTCATCAACCTCTTCCTCTCCCTGCTCACCCTCTTCAGGGCATCCGATTCC

Alignment

ORF - retro_hvul_78 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.44 %
• Parental protein coverage: 71.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLCPLRYYHQKHPVNLILLGIFTVSISFAVGMTCAFTSGKIILEAAILTAVVVISLTAYTFWAAKRGHDF
          VLCPL.YY.Q.HPVNL.LL..FTV.ISFAVG.TC.FT.G..ILE.AILT.VVV.SLTAYTFWAA..GH.F
Retrocopy VLCPLYYYYQRHPVNLLLLALFTVAISFAVGFTCVFTKGEVILESAILTTVVVVSLTAYTFWAASHGHNF

Parental  NFLGPFLFGALMVLMMFSLIQIFFPLGKISVMIYGAVASIIFCGYIIFDTDNIIKRYTYDEYIWAAVSLY
          NFLGPFLF.A.M.LM.F.L.Q.FFPLG.IS.M.Y...A...F.GYII.DTDN.IKRY.YDEY.WAAV.LY
Retrocopy NFLGPFLFVAVMILMVFTLSQAFFPLGRISLMVYSWLAALVFYGYIIYDTDNLIKRYSYDEYVWAAVALY

Parental  LDIINLFLNLMQILRAADS
          LD.INLFL.L....RA.DS
Retrocopy LDVINLFLSLLTLFRASDS

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_78 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_34672	3 retrocopies	retro_hvul_74, retro_hvul_78 , retro_hvul_79,