RetrogeneDB ID: retro_hvul_46

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 2:421785459..421786677(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_32341
• Aliases: None
• Description: None

Sequence

>retro_hvul_46
CCCATCTCCCTCGTTGGCCCGACGCCGGCGGACCTCGAGAGCACGGCGCAGCTCGAGAAGCACCTGCGTCAAGCTGGCCT
GTACGAGAGCGCTGAGGAGACGGCTGCCCGCGAGGATGTGCTGCGCGACCTCCAGGGCGTCGTCGACCGCTGGGTGAAGC
GGCTCACGACTCAGCGAGAGTACCCCGACGGCATGGCCGAGCATGCGACCGCTTTGCTCCTCCCCTTCGGCTCGTACCGC
CTCGGCGTCCATGGCCGCGGCTCCGACATCGACGCCCTCGTCGTCGGGCCCGCCTACGTCGACCGCCACCACGACTTCTT
CGACGTGCTGGGCGGCGTGCTGGCCGAGACTGAGGCTGTGACGGAGCTACAGCTGGTTCCCGGCGCGTACGTGCCGGTCA
TCAAGATGAGGTTCCGCGGCGTGCAGGTGGACCTCCTCTACGCCAGCGTCTGCCTCCCTGTGGTGCCGAGCGATCTGGAC
CTGCACGGCCGCTCCGTGCTCCGCGGCCTGGACATGGCCACCGTCCGCAGCCTCAACGGCGTCCGCGTCGCCGACGAGAT
CATCCGCCTGGTCCCGGACGCCGGCGCCTTCCGCACGACGCTGCGCTGTGTGAAGCATTGGGCCAAGGCGAGGGGCATCT
ACTCCAACGCCATGGGCTTCATCGGCGGCGTGGGGTGGGCCATCCTCGTGGCGCGCGTGTGCCAGCTCTACCCCAACGCC
GCGCCCAGCATGCTCGTGCCGCGCTTCTTCCGGATCTTCTCGCAGTGGAAGTGGCCCAACCCGGTGATGCTGCGGGAGAT
CGAGCACGACGACGACGGCGGCGAGATGCCGCTTGGGCTCCCCGTGTGGGACCCGCGGAGGAACCCCCGCGACGGGAGCC
ACCTCATGCCCGTCATCACGCCGGCATACCCCTGCATGAACTCGTGCTACAACGTCTCCCGCGCCACCCTGCGAACCATG
ACAACGGAGTTCGACGCCGCGCACAAGGCTTGCCAGGAGATAGCCGCCGCCGGCGCGTGGGACGCGCTCTTCAGGCCGTT
CAATTTCTTCAAGGCGTACAGCAACTACCTTCGGGTGGACGTGAAGGTGGCCGGCGGGGAGGAGGATCTCCGGGAGTGGA
AGGGGTGGGTCGAGTCGCGGATGAGGCAGCTGGTGGTCAGGGTCGAGATGGCCACGGCCGGCATGCTGCTCTGCCATCCG
CACCCGCAAGCCTACGCC

Alignment

ORF - retro_hvul_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.46 %
• Parental protein coverage: 57.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PISLAGPLDADVQRTAELNKFLVEAGLYESADESARREEVLGELDKIVKVWVKQLTSQRGYTDQMVEEAN
          PISL.GP..............L..AGLYESA.E.A.RE.VL..L...V..WVK.LT.QR.Y.D.M.E.A.
Retrocopy PISLVGPTXXXXXXXXXXXXXLRQAGLYESAEETAAREDVLRDLQGVVDRWVKRLTTQREYPDGMAEHAT

Parental  AVLFTFGSYRLGVHGPGADIDTLCVGPSYVNREEDFFIVLHDILAQTEDVSQLQPVPDAHVPVMKFKFHG
          A.L..FGSYRLGVHG.G.DID.L.VGP.YV.R..DFF.VL...LA.TE.V..LQ.VP.A.VPV.K..F.G
Retrocopy ALLLPFGSYRLGVHGRGSDIDALVVGPAYVDRHHDFFDVLGGVLAETEAVTELQLVPGAYVPVIKMRFRG

Parental  ISIDLLYASVSLLVVPSDLDISQEAVLYDIDEATVRSLTGCRVADQILRLVPNIESFRTTLRCLKHWARR
          ...DLLYASV.L.VVPSDLD.....VL...D.ATVRSL.G.RVAD.I.RLVP....FRTTLRC.KHWA..
Retrocopy VQVDLLYASVCLPVVPSDLDLHGRSVLRGLDMATVRSLNGVRVADEIIRLVPDAGAFRTTLRCVKHWAKA

Parental  RGVYSNVTGFLGGVNWALLVARVCQLYPNAVPSMLVSRFFRVFTQWRWPTPVMLCAIEEEELG--FPVWD
          RG.YSN..GF.GGV.WA.LVARVCQLYPNA.PSMLV.RFFR.F.QW.WP.PVML..IE....G...P...
Retrocopy RGIYSNAMGFIGGVGWAILVARVCQLYPNAAPSMLVPRFFRIFSQWKWPNPVMLREIEHDDDGGEMPLGL

Parental  PRKNPR----DRTHHMPIITPAYPCMNSSYNVSTSTLRVMIEQFQFGNKICQEIEMNKASWSALFEPFNF
          P...PR....D..H.MP.ITPAYPCMNS.YNVS..TLR.M...F....K.CQEI......W.ALF.PFNF
Retrocopy PVWDPRRNPRDGSHLMPVITPAYPCMNSCYNVSRATLRTMTTEFDAAHKACQEIAA-AGAWDALFRPFNF

Parental  FEAYKNYLQVDI-IAEDDEDLRLWKGWVESRLRQLTLKIERDTYGKLQCHPYPYEYA
          F.AY.NYL.VD...A...EDLR.WKGWVESR.RQL....E..T.G.L.CHP.P..YA
Retrocopy FKAYSNYLRVDVKVAGGEEDLREWKGWVESRMRQLVVRVEMATAGMLLCHPHPQAYA

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_46 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
Zea mays	GRMZM2G109009	1 retrocopy	retro_zmay_18,
Hordeum vulgare	MLOC_32341	1 retrocopy	retro_hvul_46 ,
Sorghum bicolor	Sb10g022090	1 retrocopy	retro_sbic_8,