RetrogeneDB ID: retro_hvul_92

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:320738227..320739217(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_81876
• Aliases: None
• Description: None

Sequence

>retro_hvul_92
GCGGCCCTCCCCACCGACGGGTCCCGCGCCGCCTCCCTCGGCGCCATCCCGAGCGGCCAAGGCCGCCACACCGTCGGCGA
GAGGTACCTCCACGACGGCGCCGAGACGCTGCCGGAGTCCGTGGACTGGAGGGCGAAGGGCGCCGTGGCCCCCGTGAAGA
ACCAGGGCCAGTGCGGCAGCTGCTGGGCGTTCTCGGCGGTCGGCGCGGTGGAAGGCATCAACAAGATCGTCACGGGCGAC
CTGGTGACGCTGTCGGAGCAGGAGCTGGTGGAGTGCGCAAGGAACGGGCAGAACAGCGGGTGCAACGGCGGGATGATGGA
GGACGCGTTCGACTTCATCGCCCGGAACGGCGGCATCGACACGGAGGCGGACTACCCCTACACCGCCAAGGACGGCAGGT
GCGACCTCGCCAAGAGGAGCCGCACTGTGGTGTCCATCGACGGCTTCGAGTCGGTGCCGGAGAACGACGAGCTGTCGCTG
AAGAAAGCAGTGGCGCACCAGCCCGTGAGCGTGGGCATCGAGGCCGGCGGCCCCGAGTTCCAGCTGTACGAGTCCGGGGT
GTTCATCGGCAGGTGCGGCACGGAGCTGGACCACGGCGTGGTGGCGGTGGGGTACGGCACCGACAATGGCAGGGACTACT
GGAGCGTGCGCAACTCATGGGGGGCAGGCTGGGGCGAGGGCGGCTACATCCGGATGGAGCGCAACGTCACCGCGCGCACC
GGCAAGTGCGGCATCGCCATGATGGCGTCCTACCCCGTCAAGAACGGGCCTAACCCGTCGCCCAAGCCAAACCCGCCGAA
GCCGAAACCGGTGGCCTGCGACCGCCACAGCAAGTGTCCGGCGGGGAGCACCTGCTGCTGCACCCACGGCGTCAGGAAGA
CGTGCTTCGTCTGGGGGTGCTGCCCTGCCAAGGGCGCCGTCTGCTGCAAGGACGGCGCTACCTGCTGCCCCTCGGACTAC
CCCGTCTGCAACGACCAGAATCGCACTTGC

Alignment

ORF - retro_hvul_92 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.46 %
• Parental protein coverage: 67.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADLTNEEYRSTYLGARTKPDRERKLSARYQAADNDELPESVDWRKKGAVGAVKDQGGCGSCWAFSAIAAV
          A.L.....R...LGA............RY.......LPESVDWR.KGAV..VK.QG.CGSCWAFSA..AV
Retrocopy AALPTDGSRAASLGAIPSGQGRHTVGERYLHDGAETLPESVDWRAKGAVAPVKNQGQCGSCWAFSAVGAV

Parental  EGINQIVTGDMIPLSEQELVDCDTS-YNQGCNGGLMDYAFEFIINNGGIDSEEDYPYKERDNRCDANKKN
          EGIN.IVTGD...LSEQELV.C.....N.GCNGG.M..AF.FI..NGGID.E.DYPY...D.RCD..K..
Retrocopy EGINKIVTGDLVTLSEQELVECARNGQNSGCNGGMMEDAFDFIARNGGIDTEADYPYTAKDGRCDLAKRS

Parental  AKVVTIDGYEDVPVNSEKSLQKAVANQPISVAIEAGGRAFQLYKSGIFTGTCGTALDHGVAAVGYGTENG
          ..VV.IDG.E.VP.N.E.SL.KAVA.QP.SV.IEAGG..FQLY.SG.F.G.CGT.LDHGV.AVGYGT.NG
Retrocopy RTVVSIDGFESVPENDELSLKKAVAHQPVSVGIEAGGPEFQLYESGVFIGRCGTELDHGVVAVGYGTDNG

Parental  KDYWLVRNSWGSVWGEDGYIRMERNIKASSGKCGIAVEPSYPTKTGENPPNPGPTPPSPAPPSSVCDSYN
          .DYW.VRNSWG..WGE.GYIRMERN..A..GKCGIA...SYP.K.G.N.P.P.P.PP.P.P....CD...
Retrocopy RDYWSVRNSWGAGWGEGGYIRMERNVTARTGKCGIAMMASYPVKNGPN-PSPKPNPPKPKPVA--CDRHS

Parental  ECPASTTCCCIYEYGKECFAWGCCPLEGATCCDDHYSCCPHNYPICNTKQGTC
          .CPA..TCCC.....K.CF.WGCCP..GA.CC.D...CCP..YP.CN....TC
Retrocopy KCPAGSTCCCTHGVRKTCFVWGCCPAKGAVCCKDGATCCPSDYPVCNDQNRTC

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_92 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_73076	2 retrocopies	retro_hvul_23, retro_hvul_68,
Hordeum vulgare	MLOC_81876	2 retrocopies	retro_hvul_49, retro_hvul_92 ,