RetrogeneDB ID: retro_hvul_65

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 4:524132830..524133655(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_16329
• Aliases: None
• Description: None

Sequence

>retro_hvul_65
CCAAAGCCCGCCTGCGCCAGGGCCTTCGCCGCCCAGGGCTGCCCGCTCTGCCTCGCCGTCTTCCCTAGCGCCGGCTCCCT
CCGCGCCCACAGCCCCACCTGTCACCTCTCTCGTGCTCCGGTTCCCTCGATGCCTATGCCAAGAACGCCCGTCGGCGGTG
CGGTGGCGCTGGGGTGCAAAATGGTGGGCGCCGGCAACGACGGGACGCTGGACGTGTGCGCGCGCGTCTGCGTCATCGAC
GAGCACGAGGCCATCGTCTACGAGAAGTTCGTGAGGCCGCTCCTCCCGGTGACGCACTACCGGTACGAGACCACGGGGAT
CCGCCCCGAGCACCTTCGGGACGCGCTGGCGGTGAAGATGGTCCAGCGGCAGGTGGAGGACATCCTCCTCAACGGCGAGC
AGCCATGGAAGGTCCGGTCCTCCCGCGGCGCGGCCAGGCTCCTCGTCGGGCACGGCCTGGAGCACGATCTCGACGCGCTG
GGCATGGACTATCCGGCGTACCTGAAGCGGGACACGGCGGTATACCCGCCGCTGATGAAGACGAGCGCCAGGCTGATGAG
CAACTCGCTCCGGTTCCTCACTCAGAGCTGCCTCGGCTATGACATCCAGACGGGCCACCAGCATCCCTACGAGGACTGCG
TGGCGGCCATGCGGCTGTACAAGAAGATGCGCGCGATGAGGCACGGCCGGCCCAACAACGTCGGAGACGGCGATGGGTGC
GCCGCGAAGCCATTCCCGACGTGGAGGCAGCGGGAGCTGGAGCGCATGTCGCCGGAGGAGCTCCTCAGCATGTCCAAGCC
CGACTACCACTGCTGGTGCCTCGAC

Alignment

ORF - retro_hvul_65 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.04 %
• Parental protein coverage: 80.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKAECARVFSARGCSICLNIFDSPATARYHRHTCQYSRAA----PMPKGGAGGRAVAMACKMVGGGSDGS
          PK..CAR.F.A.GC..CL..F.S....R.H..TC..SRA.....PMP....GG.AVA..CKMVG.G.DG.
Retrocopy PKPACARAFAAQGCPLCLAVFPSAGSLRAHSPTCHLSRAPVPSMPMPRTPVGG-AVALGCKMVGAGNDGT

Parental  VDLCARVCLVGEDENIIFQTYVKPTAPVTNYRYEVTGIRPEYLRDAMPLKLVQRRIQDILCNGEPLWKIR
          .D.CARVC...E.E.I.....V.P..PVT.YRYE.TGIRPE.LRDA...K.VQR...DIL.NGE..WK.R
Retrocopy LDVCARVCVIDEHEAIVYEKFVRPLLPVTHYRYETTGIRPEHLRDALAVKMVQRQVEDILLNGEQPWKVR

Parental  PRSYGRARILVGHIVDHDLERLGLEYPAFMIRDTAKYPPLMKTTK--LSNTLKYLAQAYLGYDVHTGIQD
          ..S.G.AR.LVGH...HDL..LG..YPA...RDTA.YPPLMKT.....SN.L..L.Q..LGYD..TG.Q.
Retrocopy -SSRGAARLLVGHGLEHDLDALGMDYPAYLKRDTAVYPPLMKTSARLMSNSLRFLTQSCLGYDIQTGHQH

Parental  PYEDCVAAMRLYIRMRSQAH--PRDYATGSGEVQNNYPAWRQRELERMSPEELLALSGSDYYCWCLD
          PYEDCVAAMRLY..MR...H..P.....G.G......P.WRQRELERMSPEELL..S..DY.CWCLD
Retrocopy PYEDCVAAMRLYKKMRAMRHGRPNNVGDGDGCAAKPFPTWRQRELERMSPEELLSMSKPDYHCWCLD

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_65 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_16329	1 retrocopy	retro_hvul_65 ,
Oryza nivara	ONIVA02G32440	1 retrocopy	retro_oniv_22,
Oryza punctata	OPUNC02G27250	1 retrocopy	retro_opun_30,
Oryza sativa japonica	OS02G0709000	1 retrocopy	retro_osat_50,