RetrogeneDB ID: retro_hvul_63

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 4:243564710..243565484(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_65248
• Aliases: None
• Description: None

Sequence

>retro_hvul_63
GGTTACGCGGTGGAGTGCAGCGTGACGATGCGCGGCACCGGCGTTCGGCTCGCGCAGGCCGGCTACGCCGTCTACGGCAT
GGACTATGAGGGCCACGGCAAGTCGGACGGCCTCAGGGGCTACGTCCCCTCCTTTGACGTCCTCCTCGGCGACTGCGCCG
CCTACTTCACCGCCGTCGTTGCTAATGCTAACCAAGCAGCAGGGCCGCCGCTGCCACGGTTCCTGCTGGGCGAGTCCATG
GGCGGCGCGGTGGCGCTCCTCCTCCACCGGGCGCGGCCGACCTACTGGACGGGCGCCGTGCTGGTGGCGCCCATGTGCAA
GATCACGGAGGAGATGAAGCCGCACCCTGCGGTGATCAAGGTGCTGGAGGCCGTGACCAGGTTCATCCCGACGTGGAAGG
TGGTGCCCACCCGGAACGTCATCGGAGCCGCCTACCGGACGCAGGCCAAGCGCGACGAGATCCGCCGGAACCCCTACTGC
TACAAGGGCTGGCCGCGCCTCAAGACGGCGGAGGAGCTCCTCCGGGCCAGCGTCCGCGTGGAGAGCGAGGTGCTCACGCA
GGTGACGCTGCCCTTCCTCGTCGTGCACGGGGGAGGCGACAGGGTCACGGACCCCTCCATCAGCCAGCACCTCTGCCGGG
AGGCGCCCAGCACGGACAAGACGCTCAAGCTCTACCCGGGCATGTGGCACGCGCTCACCTCCGGCGAGCTGCCCGAGAAC
ATCGACAAGGTCTTCATCGACATCATCGCATGGCTCGATCACAGGTCCGGTCCG

Alignment

ORF - retro_hvul_63 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.87 %
• Parental protein coverage: 73.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYAVECSVTMRGTGVRLAQAGYAVYGVDFEGHGRSEGLQGYVPSFDVLVADTDAFFAAVVAST---ANTD
          GYAVECSVTMRGTGVRLAQAGYAVYG.D.EGHG.S.GL.GYVPSFDVL..D..A.F.AVVA.....A...
Retrocopy GYAVECSVTMRGTGVRLAQAGYAVYGMDYEGHGKSDGLRGYVPSFDVLLGDCAAYFTAVVANANQAAGPP

Parental  LPRFLLGESMGGAVALLLHRMRPSYWTGAVLVAPMCKIADEMRPHPVVVSVLKLMTNIIPTWKIVPTTDV
          LPRFLLGESMGGAVALLLHR.RP.YWTGAVLVAPMCKI..EM.PHP.V..VL...T..IPTWK.VPT..V
Retrocopy LPRFLLGESMGGAVALLLHRARPTYWTGAVLVAPMCKITEEMKPHPAVIKVLEAVTRFIPTWKVVPTRNV

Parental  IDAAYRMQEKRDEIRNNPHCYQGKPRLKTAYELLRVSLNLENNVLPKVSLPFLIVHGGDDKVTDPSVSDL
          I.AAYR.Q.KRDEIR.NP.CY.G.PRLKTA.ELLR.S...E..VL..V.LPFL.VHGG.D.VTDPS.S..
Retrocopy IGAAYRTQAKRDEIRRNPYCYKGWPRLKTAEELLRASVRVESEVLTQVTLPFLVVHGGGDRVTDPSISQH

Parental  LFRSAVSQDKKLNLYPGMWHALTSGESPENIHIVFQDIIAWLDQRSFP
          L.R.A.S.DK.L.LYPGMWHALTSGE.PENI..VF.DIIAWLD.RS.P
Retrocopy LCREAPSTDKTLKLYPGMWHALTSGELPENIDKVFIDIIAWLDHRSGP

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_63 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_65248	1 retrocopy	retro_hvul_63 ,