RetrogeneDB ID: retro_hvul_52

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 3:10613082..10613562(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_10618
• Aliases: None
• Description: None

Sequence

>retro_hvul_52
TCATCGTCATCCGCCAAGCCATGCCATCAGCAACCCGCCCCAACTTCACGGCCGGCGGCTAAACCGTCCACATCCGCGCC
TGCGCCTGCCGCCGTCGTCAGATTCTCCGACGACACGGCGCGGCTACAGAAGATCAACGATGTGAGGAGGTCCACCGTCG
GGCGACAGATGAAAACCGTAATCGACCTGCTCGACAAGACGAGGGAAGCTCTTACGGCGCATCAGATCAACGAACAGACC
TACGTCGACATCGACGGCAACAGGACCCTCGCCGAGAGCCTGAGGAACAACCCCAAGGTGCGCTTCGACGGGCAGCGCTT
CTCGTACAAGCCCACGCACGACGTCGCGGGCAAAGCCGAGCTGCTTACGCTGATCAAGAGCTTCCCCGACGGCCTCCCGG
CTTCGGAGGTGAAGAAGGCCTATCCGGCCGTGGAGGACGACCTGCGGGCTCTCGGATCCTCGGGTGATGTCTATCTGCTG

Alignment

ORF - retro_hvul_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.25 %
• Parental protein coverage: 56.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AATQASTTKSHNAPRSRPANAPSAPAKQIQAI-KFSNDTERLQHINSVRKSPVGAQIKLVIELLYKTRLA
          ....A.......AP.SRPA..PS..A....A...FS.DT.RLQ.IN.VR.S.VG.Q.K.VI.LL.KTR.A
Retrocopy SSSSAKPCHQQPAPTSRPAAKPSTSAPAPAAVVRFSDDTARLQKINDVRRSTVGRQMKTVIDLLDKTREA

Parental  YTAEQINEATYVAINSNKAVFDSLTNNPKVQFDGKRFSYKSKHDLKGKDQLLHLIRRFPEGLPVVEVKDS
          .TA.QINE.TYV.I..N.....SL.NNPKV.FDG.RFSYK..HD..GK..LL.LI..FP.GLP..EVK..
Retrocopy LTAHQINEQTYVDIDGNRTLAESLRNNPKVRFDGQRFSYKPTHDVAGKAELLTLIKSFPDGLPASEVKKA

Parental  YPTVLDDLQALKASGDVWWL
          YP.V.DDL.AL..SGDV..L
Retrocopy YPAVEDDLRALGSSGDVYLL

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_52 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_06457	1 retrocopy	retro_atau_12,
Hordeum vulgare	MLOC_10618	1 retrocopy	retro_hvul_52 ,
Triticum aestivum	Traes_4AS_90C3255FC	1 retrocopy	retro_taes_119,