RetrogeneDB ID: retro_hvul_87

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 6:509466000..509466282(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_54416
• Aliases: None
• Description: None

Sequence

>retro_hvul_87
ATGAAGCTCGTGGGAAAAAGCCTCGCCCGCGACGGGCCCGGCTACGTCAAGCTATTGCCGGAGGTGGATGACGACCTGTG
GGACGCGTACAACCTCATCGCCGCCGGCGACGCCGTCGAGTCCGTCACTGTCCGGAAGATCACGAGGTCCGTAGGCCGCG
ACGCGGAGCGGGTGAAGCTGACGCTGGAGGTGGTGGTGGAGTCGACGGACTACGACAAGGACGGCTCCGTCCTGCGCGTC
CGCGGCAAGAACCTCACCAAGAACGAGCACGTCCAGATCGGC

Alignment

ORF - retro_hvul_87 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLVHRNLARNGPGSAKLLPEEEDDLWHAYNLIAVGDSLQAVTVRKVLRDSASGGRDAERVKLKLEIVVE
          MKLV...LAR.GPG..KLLPE..DDLW.AYNLIA.GD....VTVRK..R...S.GRDAERVKL.LE.VVE
Retrocopy MKLVGKSLARDGPGYVKLLPEVDDDLWDAYNLIAAGDAVESVTVRKITR---SVGRDAERVKLTLEVVVE

Parental  SVDYDKEGNVLRVRGKNITENDHVKIG
          S.DYDK.G.VLRVRGKN.T.N.HV.IG
Retrocopy STDYDKDGSVLRVRGKNLTKNEHVQIG

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_87 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT4G27650	1 retrocopy	retro_atha_7,
Brassica oleracea	Bo7g111550	1 retrocopy	retro_bole_15,
Brassica rapa	Bra019037	1 retrocopy	retro_brap_29,
Hordeum vulgare	MLOC_54416	1 retrocopy	retro_hvul_87 ,
Theobroma cacao	TCM_025327	1 retrocopy	retro_tcac_21,
Vitis vinifera	VIT_04s0023g00140	1 retrocopy	retro_vvin_2,