RetrogeneDB ID: retro_hvul_49

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 2:616046622..616047855(+)
• 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_49
CGGACGGAGGCGGACGTGCGGGCGATGTTCGACGCGTGGCTGGCGCGGCATGGCCGCACTTACAACGCGCTCGCCGAGTA
CGTCCACCGTTTCCGCGCGTTCCGGGACAACCTCGACTTCGTCGACGCCCACAACGCCCGTGCCGTGCAACGCGGCGGGT
TCCGCCTCGGGATGAACCGCTTCGCCGACCTCACCAACGCCGAGTTCCGCGCCGCCTACCTCGGCTCCAGCACGGCTGGC
AGGGGCCGCAACGCCGTCGGCGAGCGGTACAGGTACCGAGCGGAAGACGTGCTGCCGGAGTCCGTGGACTGGAGGGAGAA
GGGCGCGGTGGCGCCCGTGAAGAACCAGGGCCATTGCGGCAGCTGCTGGGCCTTCTCCACGGTCGCCGCCGTGGAAGGCG
TCAACAAGATCGTCACGGGCGACCTCGTGACGCTGTCGGAGCAGGAGCTCCTGGACTGCTCACGCAACGGTCAGAACAAT
GGGTGCAACGGCGGCATCATGGACGACGCCTTCGACTTCATCGTCCGGAACGGCGGCATCGACACCGAGAAGGACTACCC
CTACGCCGCCAAGGAAGGCAAGTGCGACCTCGCCAAGAAGGCCCGCACGGTCGTCTCCATCGACGGGTTCGAGGACGTGC
CCGACGACGACGAGGCGTCGCTGATGAAGGCCGTGGCGCACCAGCCCGTGAGCGTCGCCATCGAGGCCGGCGGGCGCGAG
TTCCAGCTCTACGAGTCCGGGGTCTTCACGGGCCGGTGCGGCACGGAGCTGGACCATGCCGTGCTCGCTGTGGGCTATGG
CACCGGCACGGAGGCCGACGGCGGCAAGGACTTCTGGCTCGTGCGCAACTCGTGGGGTCCGGGCTGGGGCGAGGGCGGCT
ACATCCGGATGGAGCGCAATGTGACCGCGCGCGCCGGCAAGTGCGGCATCGCCATGTTCGCGTCCTACCCCGTCAAGAAC
GGGCCCAACCCCAAGCCAATACCACCGGCGCCGGAGGAGAAGTGTGATCGCTACAGCTCGTGTCCGGCGGGGAGCACGTG
TTGCTGCACGTACGGCGTGAGGAGCGTGTGCCTGGCATGGGGGTGCTGCCCGGCCAAGGGAGCCACCTGCTGCCGGGACC
GGACGACCTGCTGCCCGTCGGAGTACCCCGTCTGCAACGCTGGAAAACGAACCTGCGCCAAGAGCAATGGAAGTCCGTAC
ACCGTGGATGCGCTGCCCCGGACGCCGGCGAAG

Alignment

ORF - retro_hvul_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.33 %
• Parental protein coverage: 83.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSEEEVRRMYAEWMAEHGSTYNAIGEEERRFEAFRDNLRYIDQHNAAADAGVHSFRLGLNRFADLTNEEY
          R.E..VR.M...W.A.HG.TYNA..E...RF.AFRDNL...D.HNA.A......FRLG.NRFADLTN.E.
Retrocopy RTEADVRAMFDAWLARHGRTYNALAEYVHRFRAFRDNLDFVDAHNARA-VQRGGFRLGMNRFADLTNAEF

Parental  RSTYLGARTKPDRERKLSARYQAADNDELPESVDWRKKGAVGAVKDQGGCGSCWAFSAIAAVEGINQIVT
          R..YLG..T..........RY.....D.LPESVDWR.KGAV..VK.QG.CGSCWAFS..AAVEG.N.IVT
Retrocopy RAAYLGSSTAGRGRNAVGERYRYRAEDVLPESVDWREKGAVAPVKNQGHCGSCWAFSTVAAVEGVNKIVT

Parental  GDMIPLSEQELVDCDTS-YNQGCNGGLMDYAFEFIINNGGIDSEEDYPYKERDNRCDANKKNAKVVTIDG
          GD...LSEQEL.DC.....N.GCNGG.MD.AF.FI..NGGID.E.DYPY......CD..KK...VV.IDG
Retrocopy GDLVTLSEQELLDCSRNGQNNGCNGGIMDDAFDFIVRNGGIDTEKDYPYAAKEGKCDLAKKARTVVSIDG

Parental  YEDVPVNSEKSLQKAVANQPISVAIEAGGRAFQLYKSGIFTGTCGTALDHGVAAVGYGT----ENGKDYW
          .EDVP...E.SL.KAVA.QP.SVAIEAGGR.FQLY.SG.FTG.CGT.LDH.V.AVGYGT......GKD.W
Retrocopy FEDVPDDDEASLMKAVAHQPVSVAIEAGGREFQLYESGVFTGRCGTELDHAVLAVGYGTGTEADGGKDFW

Parental  LVRNSWGSVWGEDGYIRMERNIKASSGKCGIAVEPSYPTKTGENPPNPGPTPPSPAPPSSVCDSYNECPA
          LVRNSWG..WGE.GYIRMERN..A..GKCGIA...SYP.K.G...PNP.P.PP.P......CD.Y..CPA
Retrocopy LVRNSWGPGWGEGGYIRMERNVTARAGKCGIAMFASYPVKNG---PNPKPIPPAP---EEKCDRYSSCPA

Parental  STTCCCIYEYGKECFAWGCCPLEGATCCDDHYSCCPHNYPICNTKQGTCLAAKDSPLSVKAQRRTLAK
          ..TCCC.Y.....C.AWGCCP..GATCC.D...CCP..YP.CN....TC.....SP..V.A..RT.AK
Retrocopy GSTCCCTYGVRSVCLAWGCCPAKGATCCRDRTTCCPSEYPVCNAGKRTCAKSNGSPYTVDALPRTPAK

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_49 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,