RetrogeneDB ID: retro_hvul_23

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 3:500030528..500031545(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_25678
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_73076
• Aliases: None
• Description: None

Sequence

>retro_hvul_23
ATGGACTTCGGCGACCACGACCTGGCGTCGGAGGACTCCCTATGGGCGCTGTACGAGCGCTGGCGGGAGCAGCACACCGT
GGCGCGCGACCTGGGCGAGAAGGCCCGACGCTTCAACGTGTTCAGGGAGAACGTCCGCCTCATCCACGAGTTCAACCGCG
GTGACGCCCCCTACAAGCTCCGCCTCAACCGCTTCGGCGACATGACCGCCGACGAGTTCCGCCGCGCCTACGCCTCCTCC
CGCGTCTCTCACCACCGCATGTTCAGCCTTAAGGAGGGTGGTGGCGGTTTCATGCACGGCAGCGCTGCCTCCGTCCGGGA
CGTGCCGCCGTCGGTGGACTGGCGGCAGAAGGGCGCGGTGACCGCCGTCAAGGACCAAGGGCAGTGCGGCAGCTGCTGGG
CTTTCTCGACGATCGCGGCCGTGGAGGGCATCAACGCTATCCGCTCTAAGAACCTCACGTCTCTGTCCGAGCAGCAGCTC
GTGGACTGCGACACGAAGTCCAACGCCGGCTGCAACGGCGGCCTCATGGACTACGCCTTCCAGTACATCGCCAAGCATGG
CGGGGTGGCCGCCGAGGACGCGTACCCCTACAAGGCCAGGCAGGCCTCCTCCTGCAACAAGAAGCCGTCCGCCGTGGTCA
CCATCGACGGGTATGAGGACGTGCCCGCCAACGACGAAACCGCGCTGAAGAAGGCGGTGGCTGCACAGCCAGTGGCCGTG
GCCATCGAGGCTAGCGGGTCGCACTTCCAGTTCTACTCGGAGGGGGTGTTCGCGGGCAAGTGCGGGACGGAGCTGGACCA
TGGCGTGGCGGCGGTGGGGTACGGCACCACCGTGGACGGCACCAAGTATTGGATCGTGAAAAACTCATGGGGGCCGGAGT
GGGGTGAGAAGGGATACATCCGCATGAAGCGCGATGTGAAGGACAAGGAAGGGCTCTGCGGGATCGCCATGGAGGCGTCC
TACCCAGTCAAGACCTCAGCCAACCCGAAGCATGCCGGTGCCCATGACGAGCTCTGA

Alignment

ORF - retro_hvul_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.12 %
• Parental protein coverage: 93.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTEKDLASEESLRGLYERWRSHYTVSRRGLGADAEERRFNVFKQNARYVHEGNKRDMPFRLALNKFADMT
          F...DLASE.SL..LYERWR...TV.R..LG..A..RRFNVF..N.R..HE.N..D.P..L.LN.F.DMT
Retrocopy FGDHDLASEDSLWALYERWREQHTVAR-DLGEKA--RRFNVFRENVRLIHEFNRGDAPYKLRLNRFGDMT

Parental  TDEFRRTYAGSRVRHHLSLSGGRRGDGGFRYGDADNL---PPAVDWRQKGAVTAIKDQGQCGSCWAFSTI
          .DEFRR.YA.SRV.HH...S....G.GGF..G.A......PP.VDWRQKGAVTA.KDQGQCGSCWAFSTI
Retrocopy ADEFRRAYASSRVSHHRMFSL-KEGGGGFMHGSAASVRDVPPSVDWRQKGAVTAVKDQGQCGSCWAFSTI

Parental  VAVEGINKIRTGKLVSLSEQELMDCDNVNNQGCDGGLMDYAFQFIQKN-GITTESNYPYQGEQGSCDQAK
          .AVEGIN.IR...L.SLSEQ.L.DCD...N.GC.GGLMDYAFQ.I.K..G...E..YPY...Q.S....K
Retrocopy AAVEGINAIRSKNLTSLSEQQLVDCDTKSNAGCNGGLMDYAFQYIAKHGGVAAEDAYPYKARQASSCNKK

Parental  ENALAVTIDGYEDVPANDESALQKAVAGQPVSVAIDASGQDFQFYSEGVFTGECSTDLDHGVAAVGYGAT
          ..A..VTIDGYEDVPANDE.AL.KAVA.QPV.VAI.ASG..FQFYSEGVF.G.C.T.LDHGVAAVGYG.T
Retrocopy PSAV-VTIDGYEDVPANDETALKKAVAAQPVAVAIEASGSHFQFYSEGVFAGKCGTELDHGVAAVGYGTT

Parental  RDGTKYWIVKNSWGEDWGEKGYIRMQRGVSQTEGLCGIAMQASYPTKSAPHASTVREGSHTDEL
          .DGTKYWIVKNSWG..WGEKGYIRM.R.V...EGLCGIAM.ASYP.K....A.....G.H.DEL
Retrocopy VDGTKYWIVKNSWGPEWGEKGYIRMKRDVKDKEGLCGIAMEASYPVKTS--ANPKHAGAH-DEL

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_23 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G19707	2 retrocopies	retro_bdis_26, retro_bdis_41,
Zea mays	GRMZM2G099765	1 retrocopy	retro_zmay_16,
Hordeum vulgare	MLOC_73076	2 retrocopies	retro_hvul_23 , retro_hvul_68,
Hordeum vulgare	MLOC_81876	2 retrocopies	retro_hvul_49, retro_hvul_92,
Oryza barthii	OBART11G08490	1 retrocopy	retro_obar_27,
Oryza glumaepatula	OGLUM05G09560	1 retrocopy	retro_oglu_31,
Oryza meridionalis	OMERI11G07520	1 retrocopy	retro_omer_2,
Setaria italica	Si026545m.g	1 retrocopy	retro_sita_27,