RetrogeneDB ID: retro_hvul_96

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:28831417..28832086(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_60985
• Aliases: None
• Description: None

Sequence

>retro_hvul_96
GCCCACTGCGTGCACGTGCTAGCTATACTGATCGATCGTGTTTCCGCAGGGGAGGAGGAGATGGGGCGGCTCCGGCAGGC
GGTGGAGGGGCTGGAGGTGGGCGTGCTGGTGAACAACGCCGGCGTGGCGACGCCACACGCAACGTACCTCCACGAGGCCG
ACGCGGATGCGTGGGTGAAGATGATCCGGGTGAACCTGTGCGCCGTGACGGAGGTGACGGCGGCCGTTCTGCCCGGCATG
GTGGGGCGCGGGAGGGGCGCCGTCGTCAACATCGGCTCCGGCGCGGCGGAGGCGCTGCCCTCCTACCCGCTCTACTCCGT
CTACGCCGCTACCAAGCGCTACGTGTCTCACTTCTCCAGGAGCCTCTACGTCGAGTACAGCGGCAAAGGAATCGACGTGC
AGTGCCAGGCCCCGTTGTACGTGGACACGAAGATGGTGACCAACATGGTGACGCGGGGGGCAGGCCTCCTGTCGCGGCTG
ATCGTGCCGACGTCGGACGCGTACGCCGGCGCGGCGGCGCGCTGGATCGGGTTCCGCCGCCCGGTCTGCATGCCCAACCT
CGGCCACCGGCTGCAGTGGTGCCTCTGCCACTACGTCCCGGATCGCGTACTCGCCGCGCACCGCCTCCGCGAGAACCTCC
GGCAACGGGACGTCTTCCAGCGGCTCAGG

Alignment

ORF - retro_hvul_96 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.47 %
• Parental protein coverage: 65.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AHAVQTKTVLFDFSLVSAAQGDEAMRRLREAVAGLDVGLLVNNAGVAKPGAMYLHEADVEAWARMIRVNV
          AH.V.....L.D...VSA..G.E.M.RLR.AV.GL.VG.LVNNAGVA.P.A.YLHEAD..AW..MIRVN.
Retrocopy AHCVHVLAILID--RVSA--GEEEMGRLRQAVEGLEVGVLVNNAGVATPHATYLHEADADAWVKMIRVNL

Parental  LALTEVTAAVLPGMVRRGRGAVVNLGSGSASVLPSFPLYSVYAATKRYVAEFSRSLAVEYGSSGIDVQCQ
          .A.TEVTAAVLPGMV.RGRGAVVN.GSG.A..LPS.PLYSVYAATKRYV..FSRSL.VEY...GIDVQCQ
Retrocopy CAVTEVTAAVLPGMVGRGRGAVVNIGSGAAEALPSYPLYSVYAATKRYVSHFSRSLYVEYSGKGIDVQCQ

Parental  VPFLVETNMVSSAVK--ANLILQFVL-TPDAYAYAAVRWIGHGR-LCVPNVAHRFQGWYAGLFPDFVNDA
          .P..V.T.MV...V...A.L.......T.DAYA.AA.RWIG..R..C.PN..HR.Q.......PD.V..A
Retrocopy APLYVDTKMVTNMVTRGAGLLSRLIVPTSDAYAGAAARWIGFRRPVCMPNLGHRLQWCLCHYVPDRVLAA

Parental  FRLEKNRGQRAILRRVK
          .RL..N..QR....R..
Retrocopy HRLRENLRQRDVFQRLR

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_96 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_60985	2 retrocopies	retro_hvul_73, retro_hvul_96 ,
Hordeum vulgare	MLOC_65044	1 retrocopy	retro_hvul_95,