RetrogeneDB ID: retro_hvul_71

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 4:519822348..519822915(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_65294
• Aliases: None
• Description: None

Sequence

>retro_hvul_71
GGCCGGCGATCTAAGGACTCCATCGTTGTCTACGTCGCCTTCGACGGCGCCGTCGACCAGTACTTCATGAACTACCCCGA
CAAGCTCTTCGGCAAGCCGATGGAGAGGTGCCACGTTGACGCGCAGAACCAGAAGGTACTCCGGCAGCACCTCGCCTGCG
CCGCCGTCGAGAACCAGCTCCGGGCCGACCGCGATGAGCCCTACTACGGCGCCACCATGAACGACGCCATCACGTTCTTG
AGAGATAAAGGAATCCTCGCCGCCAATCCAACCGGCAACACGTGGAAGTATGCCGGCCACGTCAGGCGGCCGTCGCAGTC
GGTGAGCATCCGTGCGATCGAGCATGACAAGTTCACGGTGATAGAGACGCCGAGCCAGCGAGTGTTGGAGGAGATCGAGC
AGAGCAAGGCCTTCTTCCAGGTGCACGAGGGCGCCGTGTACATGCACCAGGGCGTGAGCTACCTGGTCGACACGCTCGAC
CTCTCGTCCAGGACGGCCTACTGCAGCATCAGCAAATCCGAGCTCTGCTACCACACCAAGACAGAAGACTACACTGACAT
CGACGTC

Alignment

ORF - retro_hvul_71 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.03 %
• Parental protein coverage: 83.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRRAKQSLAIYVAFEGPLDQYFMKSPDKLFGKPIEHCQVDSHNPKVLGQHIACAAYEHPICLQYDENHFG
          GRR.K.S...YVAF.G..DQYFM..PDKLFGKP.E.C.VD..N.KVL.QH.ACAA.E.......DE...G
Retrocopy GRRSKDSIVVYVAFDGAVDQYFMNYPDKLFGKPMERCHVDAQNQKVLRQHLACAAVENQLRADRDEPYYG

Parental  STLDRIVTTLKDKGFLVNNPSGPFSSTMWNYIGPEKNPSQTISIRAIEHDKYKVIDKLNNRLLEEIEESK
          .T.....T.L.DKG.L..NP.G......W.Y.G....PSQ..SIRAIEHDK..VI.....R.LEEIE.SK
Retrocopy ATMNDAITFLRDKGILAANPTG----NTWKYAGHVRRPSQSVSIRAIEHDKFTVIETPSQRVLEEIEQSK

Parental  AFFQVYEGAIYMHQGVNYLVEEFDLSSRTAFC--RKVDVKYYTKTRDYTDINV
          AFFQV.EGA.YMHQGV.YLV...DLSSRTA.C...K....Y.TKT.DYTDI.V
Retrocopy AFFQVHEGAVYMHQGVSYLVDTLDLSSRTAYCSISKSELCYHTKTEDYTDIDV

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_71 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_65294	1 retrocopy	retro_hvul_71 ,