RetrogeneDB ID: retro_hvul_13

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: Pt:52114..53611(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: EPlHVUG00000010007
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_70791
• Aliases: None
• Description: None

Sequence

>retro_hvul_13
ATGAGAACCAATCCTACTACTTCTCGTCCCGGGGTTTCCACAAGTGAAGAAAAAAGTACAGGTCGTATCGATCAAATTAT
TGGACCCGTGCTGGATGTCACTTTTCCCCCGGGCAAGTTACCTTATATTTATAACGCTTTAGTAGTCCAGAGTAGAGACA
CTGCCGATAAGCAAATTAATGTGACTTGTGAGGTACAACAATTATTAGGAAATAATCGAGTTAGAGCTGTAGCTATGAGT
GCTACGGACGGGTTGATGAGAGGAATGGAAGTGATTGACACGGGAGCTCCTCTCAGTGTTCCGGTCGGTGGAGCTACTCT
CGGACGAATTTTCAACGTTCTTGGGGAGCCTGTTGACAATTTGGGTCCTGTAGATAGTAGTGCAACGTTCCCTATTCATA
GATCTGCGCCTGCCTTTATCGAGTTAGATACGAAATTATCCATCTTTGAAACAGGTATTAAGGTCGTCGATCTTTTAGCT
CCTTATCGACGTGGAGGAAAAATAGGACTATTTGGGGGGGCTGGAGTAGGTAAAACAGTACTGATCATGGAATTAATCAA
TAACATTGCTAAAGCTCATGGGGGCGTATCCGTATTCGGTGGAGTAGGGGAACGGACTCGTGAAGGAAATGATCTTTATA
TGGAAATGAAGGAATCCGGAGTAATTAATGAAAAAAATATTGAAGAATCAAAGGTAGCTCTAGTCTATGGCCAAATGAAT
GAACCACCGGGAGCTCGTATGAGAGTTGGTTTAACTGCCCTAACTATGGCAGAATATTTCCGAGATGTTAATAAGCAAGA
CGTGCTTTTATTTATCGATAATATCTTTCGTTTTGTTCAAGCAGGATCAGAGGTATCCGCTTTATTAGGGAGAATGCCCT
CCGCAGTGGGTTATCAACCTACTCTTAGTACAGAAATGGGTTCTTTGCAAGAAAGAATTGCTTCTACTAAAAAGGGATCT
ATAACTTCGATTCAAGCAGTTTATGTACCTGCGGACGATTTGACCGACCCTGCCCCTGCCACAACATTTGCACATTTGGA
TGCTACTACCGTACTTTCCAGAGGATTAGCTTCCAAGGGTATTTATCCAGCAGTAGATCCTTTAGATTCAACATCAACTA
TGTTACAGCCTCGGATCGTTGGCAACGAACATTATGAAACTGCGCAAAGAGTTAAGGAAACTTTACAACGTTACAAAGAA
CTTCAGGACATTATCGCAATTCTTGGCTTGGATGAATTATCGGAAGAGGATCGTTTAACTGTAGCAAGAGCAAGAAAAAT
TGAGCGTTTCTTATCACAACCGTTCTTTGTGGCAGAAGTTTTTACTGGTTCTCCAGGAAAGTATGTTGCTCTTGCGGAAA
CTATTAGGGGATTTCAACTAATCCTTTCCGGAGAATTAGACGGCCTACCTGAACAGGCTTTTTATTTGGTGGGTAACATC
GATGAAGCTAGCACGAAAGCTATAACCTTAGAAGAGGAGAACAAATCGCAGAAATGA

Alignment

ORF - retro_hvul_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.42 %
• Parental protein coverage: 99.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDGTEGLVRGQKVLNTGSPITVPVGRATLGRIINVIGEPIDHKGDIKTNSYLPIHREAPAFVEQATEQQI
          M..T.GL.RG..V..TG.P..VPVG.ATLGRI.NV.GEP.D..G........PIHR.APAF.E..T...I
Retrocopy MSATDGLMRGMEVIDTGAPLSVPVGGATLGRIFNVLGEPVDNLGPVDSSATFPIHRSAPAFIELDTKLSI

Parental  LVTGIKVVDLLAPYQRGGKIGLFGGAGVGKTVLIMELINNVAKAHGGFSVFAGVGERTREGNDLYREMIE
          ..TGIKVVDLLAPY.RGGKIGLFGGAGVGKTVLIMELINN.AKAHGG.SVF.GVGERTREGNDLY.EM.E
Retrocopy FETGIKVVDLLAPYRRGGKIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGGVGERTREGNDLYMEMKE

Parental  SGVIKLDDKQSESKCALVYGQMNEPPGARARVGLTGLTVAEHFRDAEGQDVLLFIDNIFRFTQANSEVSA
          SGVI.......ESK.ALVYGQMNEPPGAR.RVGLT.LT.AE.FRD...QDVLLFIDNIFRF.QA.SEVSA
Retrocopy SGVIN-EKNIEESKVALVYGQMNEPPGARMRVGLTALTMAEYFRDVNKQDVLLFIDNIFRFVQAGSEVSA

Parental  LLGRIPSAVGYQPTLATDLGGLQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRQIS
          LLGR.PSAVGYQPTL.T..G.LQERI..TKKGSITS.QA.YVPADDLTDPAPATTFAHLDATTVLSR...
Retrocopy LLGRMPSAVGYQPTLSTEMGSLQERIASTKKGSITSIQAVYVPADDLTDPAPATTFAHLDATTVLSRGLA

Parental  ELGIYPAVDPLDSTSRMLSPHVLGQEHYNTARGVQKVLQNYKNLQDIIAILGMDELSEDDKLTVARARKI
          ..GIYPAVDPLDSTS.ML.P...G.EHY.TA..V...LQ.YK.LQDIIAILG.DELSE.D.LTVARARKI
Retrocopy SKGIYPAVDPLDSTSTMLQPRIVGNEHYETAQRVKETLQRYKELQDIIAILGLDELSEEDRLTVARARKI

Parental  QRFLSQPFHVAEVFTGAPGKYVELKEGVQSFQGVLDGKYDDLSEQAFYMVGGIEEVIAKAEKIAKEN
          .RFLSQPF.VAEVFTG.PGKYV.L.E....FQ..L.G..D.L.EQAFY.VG.I.E...KA.....EN
Retrocopy ERFLSQPFFVAEVFTGSPGKYVALAETIRGFQLILSGELDGLPEQAFYLVGNIDEASTKAITLEEEN

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_13 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00006p00059970	1 retrocopy	retro_atri_7,
Arabidopsis thaliana	AT5G08670	1 retrocopy	retro_atha_12,
Oryza sativa indica	BGIOSGA017602	2 retrocopies	retro_oind_104, retro_oind_87,
Brassica rapa	Bra006013	2 retrocopies	retro_brap_51, retro_brap_57,
Chlamydomonas reinhardtii	CHLREDRAFT_78348	1 retrocopy	retro_crei_1,
Aegilops tauschii	F775_32946	1 retrocopy	retro_atau_18,
Hordeum vulgare	MLOC_70791	1 retrocopy	retro_hvul_13 ,
Oryza glaberrima	ORGLA01G0220100	1 retrocopy	retro_ogla_47,
Triticum aestivum	TRAES3BF058700080CFD_g	2 retrocopies	retro_taes_170, retro_taes_31,