RetrogeneDB ID: retro_hvul_57

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 3:511538858..511539704(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_51268
• Aliases: None
• Description: None

Sequence

>retro_hvul_57
AATGACACCACCTACTTCGGCGCGCTGGTGGGGCGGGTGGCGAACCGGATCGCCGGCGGGCGGTTCACGATCAAGGACCA
CGCGTACCACACCTACACGAACGACGGCAACAACACGCTCCACGGCGGCCACCGCGGGTTCAACCAGGTGTTCTGGTCGG
TGCGGGAGCGGGTCACCGGCGCCTTCCCCTACATCACCTTCTACTACCGCAGCGGCGACGGCGAGGAGGGCTTCCCGGGC
GCGCTGGACGTGCTGGTGACCTACAAGATCGACGGCGACTACTCGTACAGCGTCACCATGTACGCCCGGCCGGTGGACAA
GCCGACGCCCGTGAACCTGGCGCAGCACACGTACTGGAACCTGCGCGGGCACGGGCGGGGCACCGTCCTGGACCACTCCG
TCCAGATCTTCGCGTCGGCCGTCACCCCCGTCGGCGGCGACCTGATCCCGACGGGCGCCGTGACGCCCGTCGCCGGCACG
CCCTTCGACTTCCGCGCCCCGGCGGCGGCCGGCGCGCGCATCGCGGAGGTGGAGGGCGGCTACGACATCAACTACGTCCT
GGACGGCGCGGACGCGGACGGGCAGGGGGTGCGCAAGGTGGCGGTGGTGAGCGAGGCGACGTCCGGGCGGGTGATGGAGC
TGTGGGGCGACCAGCCCGGCGTGCAGTTCTACACCGGCAACTTCCTCAAGGGCGAGCAGGGCAAGGGCGGCGCCGTGTAC
GAGAAGCACGGCGGGCTGTGCCTGGAGACGCAGGACTTCCCCGACGCCGTGCACAACCCCAAGTTCCCCACCGAGATCTA
CCGCAAAGGCCAGGTCTACAAGCACTACATGCTCTACAAGTTCTCG

Alignment

ORF - retro_hvul_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.19 %
• Parental protein coverage: 77.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGTAYFGGLIGRVANRIANARFTLDGKSYRLFPNDGNNTLHGGHRGFDKVVWTVKEHVAGGRSPFITLYY
          N.T.YFG.L.GRVANRIA..RFT.....Y....NDGNNTLHGGHRGF..V.W.V.E.V.G...P.IT.YY
Retrocopy NDTTYFGALVGRVANRIAGGRFTIKDHAYHTYTNDGNNTLHGGHRGFNQVFWSVRERVTGA-FPYITFYY

Parental  HSFDGEQGFPGDVDVHVTYQITGRHALSVRMNATARSKATPVNLAHHAYWNLGGDGSGSVLGQKIRLFAS
          .S.DGE.GFPG..DV.VTY.I.G....SV.M.A....K.TPVNLA.H.YWNL.G.G.G.VL......FAS
Retrocopy RSGDGEEGFPGALDVLVTYKIDGDYSYSVTMYARPVDKPTPVNLAQHTYWNLRGHGRGTVLDHSVQIFAS

Parental  RYTPVDAALIPTGRLAPVAGTPYDFRRPAAVGARIGGLLSRGVAGYDINYVVDG----GRGLRRVAAVRD
          ..TPV...LIPTG...PVAGTP.DFR.PAA.....G........GYDINYV.DG....G.G.R.VA.V..
Retrocopy AVTPVGGDLIPTGAVTPVAGTPFDFRAPAAA----GARIAEVEGGYDINYVLDGADADGQGVRKVAVVSE

Parental  GASGRAMELWADQPGVQFYTANGLSGVRGKGGKVYGRYGALCLETQGFPNAVNEPSFPSQIVRPGKVYRH
          ..SGR.MELW.DQPGVQFYT.N.L.G..GKGG.VY...G.LCLETQ.FP.AV..P.FP..I.R.G.VY.H
Retrocopy ATSGRVMELWGDQPGVQFYTGNFLKGEQGKGGAVYEKHGGLCLETQDFPDAVHNPKFPTEIYRKGQVYKH

Parental  HMLFRFS
          .ML..FS
Retrocopy YMLYKFS

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_57 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_51268	1 retrocopy	retro_hvul_57 ,