RetrogeneDB ID: retro_hvul_1

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:541306435..541307920(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_77827
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_55999
• Aliases: None
• Description: None

Sequence

>retro_hvul_1
ATGGTGCTTACCAGGATGAAGGAGACCGCCGAGGCCTACCTCGGCGAGAAGGTCACGCACGCCGTCGTCACCGTGCCGGC
CTACTTCAACGACGCGCAGCGACAGGCCACCAAGGACGCCGGCGTCATCGCCGGCCTCAACGTCATCCGAATCGTCAACG
AGCCCACCGCCGCCGCCATCGCCTACGGCATCGACGAGAAGGGGCCCGAGAAGAACGTCCTGGTCTTCGACCTCGGCGGC
GGCACCTTTGATGTCAGCGTGCTCTCCATCGACAATGGCGTCTTCGAGGTCCTGGCCACAAACGGCGACACGCACCTCGG
CGGTGAGGATTTCGACCAGCGCCTCATGGACTACTTCATCAAGCTCATTAAGCGGAAGCATGCCCGGGACATCACCGGTG
ACCTGCGCGCCCTGGGCAAGCTGCGGCGCGAGTGCGAGCGCGCCAAGCGTGCGCTCAGCAACCAGCACCAGGTGCGCGTC
GAGATCGAATCCCTCTTCGACGGCGTCGACTTGTCGGAGCCGCTCACCAGGGCACGGTTCGAGGAGCTCAACAACGACCT
TTTCCGCAAGACGATGGTGCCCGTGAAGAAGGCCATGGCTGACGCCGGGCTCAACAAGGCTGACATCGACGAGATCGTGC
TCGTCGGTGGCAGCACCAGGATTCCCAAGGTGCAGCAGCTCCTCAAGGACTACTTCAACGGCAAGGAACCCAACAAGGGG
GTAAACCCCGACGAGGCCGTCGCGTACGGCGCCGCCGTGCAGGCCAGCATCGTGAGCGGGCACGTCGACGAGAACACCAA
AACCATGATCCTGATCGACGTCGCGCCGCTTACACTAGGCATGGAGACGGTCGGCGGCGTCATGACGAAGCTGATCCCGA
GGAACACGGTGGTGCCGACGAAGAAGACACAGGTGTTCACCACGTACCAGGACAAGCAGACCACCGTGTCCATCAAGGTC
TACGAGGGCGAGAGGAGCATGACCAAGGACAACAGGCTCCTCGGCAAGTTTGATCTCTCTGGGATCCCGCCGGCTCCGAG
GGGCACGCCCCAAATCGAGGTGACCTTCGAGGTGGACGTCAATGGCATCCTGCACGTGAAGGCGGCGGACAAGGGAACCG
GCAAGTCGGAGAAGATCACCATCACCAACGAGGGCCGTCGGCATAGCCAGGAGGACATCGACCGGATGGTGCGCGAGGCA
GAGGAGTTCGCCGAGGCGGATCTCAAGGTCAAGGAAAGGGTCGACGCCAGGAACAAGCTAGAGTCTTACGTGTATGGCAT
CAAGGACACCGTCGACGGCAAGATGGCCGACGCCATGGACAAGGATGAGAAGAACAAGGTCGAGGATGCAATGAGGGAGG
TGAACGAGTGGCTCGACGACAACGCAGAGGCGGCAGACAAGGAGGACTATGACGAGAAGCTCCGGGAGCTGGAAGACGTG
TGCAACCCCATCATTACGGCGGTGTACCAGAGGTCCGGAGGTGCA

Alignment

ORF - retro_hvul_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.28 %
• Parental protein coverage: 74.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MILGKMKETAEAYLGKKINDAVVTVPAYFNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGLDKRGGE
          M.L..MKETAEAYLG.K...AVVTVPAYFNDAQRQATKDAGVIAGLNV.RI.NEPTAAAIAYG.D..G.E
Retrocopy MVLTRMKETAEAYLGEKVTHAVVTVPAYFNDAQRQATKDAGVIAGLNVIRIVNEPTAAAIAYGIDEKGPE

Parental  KNILVFDLGGGTFDVSILTIDNGVFEVLATNGDTHLGGEDFDHRIMDYFIKLIKKKHGKDISKDNRALGK
          KN.LVFDLGGGTFDVS.L.IDNGVFEVLATNGDTHLGGEDFD.R.MDYFIKLIK.KH..DI..D.RALGK
Retrocopy KNVLVFDLGGGTFDVSVLSIDNGVFEVLATNGDTHLGGEDFDQRLMDYFIKLIKRKHARDITGDLRALGK

Parental  LRREAERAKRALSNQHQVRVEIESLFDGTDFSEPLTRARFEELNNDLFRKTMGPVKKAMDDAGLEKTQIH
          LRRE.ERAKRALSNQHQVRVEIESLFDG.D.SEPLTRARFEELNNDLFRKTM.PVKKAM.DAGL.K..I.
Retrocopy LRRECERAKRALSNQHQVRVEIESLFDGVDLSEPLTRARFEELNNDLFRKTMVPVKKAMADAGLNKADID

Parental  EIVLVGGSTRIPKVQQLLRDYFDGKEPNKGVNPDEAVAFGAAVQGSILSGEGGDETKDILLLDVAPLTLG
          EIVLVGGSTRIPKVQQLL.DYF.GKEPNKGVNPDEAVA.GAAVQ.SI.SG.....TK...L.DVAPLTLG
Retrocopy EIVLVGGSTRIPKVQQLLKDYFNGKEPNKGVNPDEAVAYGAAVQASIVSGHVDENTKTMILIDVAPLTLG

Parental  IETVGGVMTKLIPRNTVIPTKKSQVFTTYQDQQTTVSIQVFEGERSMTKDCRLLGKFDLSGIPAAPRGTP
          .ETVGGVMTKLIPRNTV.PTKK.QVFTTYQD.QTTVSI.V.EGERSMTKD.RLLGKFDLSGIP.APRGTP
Retrocopy METVGGVMTKLIPRNTVVPTKKTQVFTTYQDKQTTVSIKVYEGERSMTKDNRLLGKFDLSGIPPAPRGTP

Parental  QIEVTFEVDANGILNVKAEDKGTGKSEKITITNEKGRLSQEEIDRMVKEAEEFAEEDKKVKERIDARNQL
          QIEVTFEVD.NGIL.VKA.DKGTGKSEKITITNE..R.SQE.IDRMV.EAEEFAE.D.KVKER.DARN.L
Retrocopy QIEVTFEVDVNGILHVKAADKGTGKSEKITITNEGRRHSQEDIDRMVREAEEFAEADLKVKERVDARNKL

Parental  ETYVYNMKNTVGDKDKLADKLESEEKEKVEEALKEALEWLDEN-QTAEKEDYEEKLKEVEAVCNPIVSAV
          E.YVY..K.TV....K.AD.....EK.KVE.A..E..EWLD.N...A.KEDY.EKL.E.E.VCNPI..AV
Retrocopy ESYVYGIKDTV--DGKMADAMDKDEKNKVEDAMREVNEWLDDNAEAADKEDYDEKLRELEDVCNPIITAV

Parental  YQRSGGA
          YQRSGGA
Retrocopy YQRSGGA

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_1 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G01477	1 retrocopy	retro_bdis_30,
Aegilops tauschii	F775_27431	1 retrocopy	retro_atau_11,
Oryza longistaminata	KN538684.1_FG046	1 retrocopy	retro_olon_13,
Hordeum vulgare	MLOC_55999	1 retrocopy	retro_hvul_1 ,
Oryza nivara	ONIVA01G37420	1 retrocopy	retro_oniv_8,
Oryza rufipogon	ORUFI02G01160	1 retrocopy	retro_oruf_18,
Sorghum bicolor	Sb04g001140	1 retrocopy	retro_sbic_39,
Triticum aestivum	Traes_6DS_A593093E1	1 retrocopy	retro_taes_72,