RetrogeneDB ID: retro_hvul_95

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:589724078..589724501(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_65044
• Aliases: None
• Description: None

Sequence

>retro_hvul_95
GTGCATGCAGGCGACGAGGCGCTGCGGCGGCTCCGGGACGCGGTGGAGGGGCTGGACGTGGGGGTCCTCGTCAACAACGC
CGGGGTGATGAGGCCGGGCGCGGCGTTCCTACACGAGGGCGACGCGGAGGCGTACGTGCGCATGATCCGCGTGAACCTGT
GGGCGCCGACGGCGATGGCCGCCGCGGTGATCCCCGGCATGGCGGCGCGGGGCAGGGGCGCCGTCGTCAACGTGGGGTCG
GGCTCCTCGGAGGCCGTCTCCTCCTTCCCGCTCCACGCCGTCTACTCCGGCACCAAGCGGTACCTCGCCAGGCTCTCCAG
GGGCCTCGCCGCCGAGTACGCGGGCAGAGGGGTCGACGTGCAGTGCCAGGCGCCGCTGTTCGTGGCGACGGAGATGATGG
CCGGCTTCTCGGGGGTCTGGCGC

Alignment

ORF - retro_hvul_95 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.21 %
• Parental protein coverage: 62.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHAGDAALRRLRDAVKKLDVGILVNNAGVAKPGAVFLHEADVEAWVRMIRVNLWAVTEVTAAVLPGMVQR
          .HAGD.ALRRLRDAV..LDVG.LVNNAGV..PGA.FLHE.D.EA.VRMIRVNLWA.T...AAV.PGM..R
Retrocopy VHAGDEALRRLRDAVEGLDVGVLVNNAGVMRPGAAFLHEGDAEAYVRMIRVNLWAPTAMAAAVIPGMAAR

Parental  GRGAVVNMGSASSEAIHSFPLHTMYSATKRYVAQFSRSLYVEYKSKGIDVQCQAPFFVATTMASGFVATW
          GRGAVVN.GS.SSEA..SFPLH..YS.TKRY.A..SR.L..EY...G.DVQCQAP.FVAT.M..GF...W
Retrocopy GRGAVVNVGSGSSEAVSSFPLHAVYSGTKRYLARLSRGLAAEYAGRGVDVQCQAPLFVATEMMAGFSGVW

Parental  R
          R
Retrocopy R

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_95 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_60985	2 retrocopies	retro_hvul_73, retro_hvul_96,
Hordeum vulgare	MLOC_65044	1 retrocopy	retro_hvul_95 ,