RetrogeneDB ID: retro_hvul_94

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:487665007..487665880(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_56431
• Aliases: None
• Description: None

Sequence

>retro_hvul_94
ATGATGAACCCGGAGATGATGCGGGTGGCGGAGGAGCAGATGCGGCGCATACCCGCCGACGACCTCGCCAGGATGCAGCG
GCAGCTCATGTCCAACCCGGACCTGCTGAAGCTCGCCACCGAGAGCATGAAGAACATGACGGCCAACGACTTCAAGCGAG
CTGCCGAGCACCTGAACCATACGCCTCCAGAGGAGATGCTCGACATGACCGAGAAAATCGCCAAGGCCAAGCCCGAGGAG
CTCGCCGCCATGAAGGCCCAAGCCGACGCACAGACGTCGTACGCGATATCCACCGCCAAGACGCTCAAGCGGGAGGGGAA
CCAGCTCCACCGCGACGGGCAGTACGCCGACGCTGCCGCCAAGTACAAGCTCGCCAGGGATAACGTGAAGAACGGCGTGC
CGTCGCCGGTCGGGCGCGATCTGCAGCTGCAGTGCAGCGTTAATCTGATGGCATGTTACCTGAAACTAGGCGAGTTTGAG
GAGTGCGTCAACGAAGGCTCGGAGGTTTTGAGCTATGACTCGGGCACCGTCAAAGCGTACTACCGAAGGGGTCAGGCATA
CAAGGAGCTGGGAAACCTCCAGGCTGCTGTTGCTGACCTAAGTAAAGCCCATGAAATGTCTCCGGACGATGAAACTGTCG
CTCAAGTTCTGACAGAGGCACAAGAAAAACTTGCAACCCAAGGGGAGGCAGCAGAAAACGTGCCAAAGGGACTTGTTATT
GAAGAAATCGTAGAGGAAGATGTTAGTTCTGATCTGTCAACCGCTCAACAGAATTCTTCTTCTTCTACTACTGAGCATAC
TGTTTCACAACCACAACCACACGACGAAGCACGAAGCTCGAGACAGTCTGATTCTTCAGAAAGCTTGATCAAT

Alignment

ORF - retro_hvul_94 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.13 %
• Parental protein coverage: 50.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMDPEMMRLAQEQMRRMSSDDLARMQQQLMSNPDLIKLASESMKNMRTEDFKRAAEQLNQTRPEEMLDMT
          MM.PEMMR.A.EQMRR...DDLARMQ.QLMSNPDL.KLA.ESMKNM...DFKRAAE.LN.T.PEEMLDMT
Retrocopy MMNPEMMRVAEEQMRRIPADDLARMQRQLMSNPDLLKLATESMKNMTANDFKRAAEHLNHTPPEEMLDMT

Parental  EKIANAKPEEFAAMKAQADAQISYALSGAKMLKQQGNELHSRGNYSGAAAKYKLAKENMKS-LPSAAGRT
          EKIA.AKPEE.AAMKAQADAQ.SYA.S.AK.LK..GN.LH..G.Y..AAAKYKLA..N.K...PS..GR.
Retrocopy EKIAKAKPEELAAMKAQADAQTSYAISTAKTLKREGNQLHRDGQYADAAAKYKLARDNVKNGVPSPVGRD

Parental  LQLQCTLNLMSCYLKSGMFEDCVNEGSEVLTYDSSNVKAYYRRGQAYKELGNLQAAVADLSKAHEISPED
          LQLQC..NLM.CYLK.G.FE.CVNEGSEVL.YDS..VKAYYRRGQAYKELGNLQAAVADLSKAHE.SP.D
Retrocopy LQLQCSVNLMACYLKLGEFEECVNEGSEVLSYDSGTVKAYYRRGQAYKELGNLQAAVADLSKAHEMSPDD

Parental  ETIAEVLRDTDEKLATEGGEA-NQPKGVVIEEIVEQD-SSELLRTQRSS----TQYAVSQPL--EGAGDS
          ET.A.VL....EKLAT.G..A.N.PKG.VIEEIVE.D.SS.L...Q..S....T...VSQP.....A..S
Retrocopy ETVAQVLTEAQEKLATQGEAAENVPKGLVIEEIVEEDVSSDLSTAQQNSSSSTTEHTVSQPQPHDEARSS

Parental  RQSDSSESLMN
          RQSDSSESL.N
Retrocopy RQSDSSESLIN

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_94 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G56980	1 retrocopy	retro_bdis_36,
Aegilops tauschii	F775_31516	1 retrocopy	retro_atau_10,
Hordeum vulgare	MLOC_56431	1 retrocopy	retro_hvul_94 ,
Oryza barthii	OBART07G03860	1 retrocopy	retro_obar_28,
Oryza glaberrima	ORGLA07G0032400	1 retrocopy	retro_ogla_27,