RetrogeneDB ID: retro_hvul_50

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 2:624463979..624464834(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_77509
• Aliases: None
• Description: None

Sequence

>retro_hvul_50
GGCAGCCTCCGTAGGGTTTTACCTGATGCGGCGCCCGAAACCGGGGAGGCGATTGATGGAATCCTGGAGGACGTAGGGCA
ACACATCCTCCCTGGACTCACACACTTCCAGAGCCCCAACTTCTTTGCCTACTACCCTGCCAACGCCAGCACTGCCGGCT
TCGTCGGCGAGATGCTCTGCGCCGGCCTCAACGTCGTACCTTTCACATGGGCCGCCTCGCCTATGGCAACCGAGCTTGAA
TGCCTCATGCTGGACTGGATGGGCAAGCTCATGTGCCTTCCGGACCGCTTCCTCTTCTCAGGCAGCGGCGGCGGCGGCGG
CGTGCTGCACGGAAGCACATGCGAGTCTGTGGTATGCACCCTTGCCGCCGCACGGGACCGCGCGCTCAAACGGCTCATGA
CCCATGAAGCCATCCTGAAGCTGGTGGTGTACGCCTCGGACCAGAGCCACACCACCTTCCAGAAGGGGGCCAGGATTGTA
GGGATCCCGCCGTCAAACTTCCGTGTCATCCCGACGTCGGCCGCGTCCAGCTACGGCCTGACCGCCGAGAGCGTCCGGGA
CGCGGTGGAGGCGGACCTCGCCAGCGGGCTCGTGCCGCTCTACCTGTGCGCCACGGTGGGCACCACCGGCGTGGGCGCGG
TCGACCCGGTGGGTGAGCTCGGGGAGGTGGCGCGGCGCTACGGGATGTGGCTCCACGTCGACGCCGCCTACGCCGGCAGC
GCGCTCATCTGCCCCGAGTTCCAGGGTTACATGGAGGGCGCGGAGCTGGCAGACTCGGTGAGCATGAACCCGCACAAGTG
GTTCCTCACCAACATGGACTGCTGCTGTCTCTGGGTGGCCACCCCATCCCAGCTC

Alignment

ORF - retro_hvul_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.18 %
• Parental protein coverage: 76.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYLKELLPDSAPNRPDTLDTLFDDIREKIIPGVTHWQSPSYFAYYPSNSSTAGFLGEMLSAAFNIVGFSW
          G.L...LPD.AP......D....D....I.PG.TH.QSP..FAYYP.N.STAGF.GEML.A..N.V.F.W
Retrocopy GSLRRVLPDAAPETGEAIDGILEDVGQHILPGLTHFQSPNFFAYYPANASTAGFVGEMLCAGLNVVPFTW

Parental  ITSPAATELEVIVLDWFAKMLKLPSQ--FLSDAPGGGVIQGTASEAVLVVLLAARDRTLKK-HGKKSLEK
          ..SP.ATELE...LDW..K...LP....F...........G...E.V...L.AARDR.LK.........K
Retrocopy AASPMATELECLMLDWMGKLMCLPDRFLFSGXXXXXXXLHGSTCESVVCTLAAARDRALKRLMTHEAILK

Parental  LVVYASDQTHSALQKACQIAGIFPENFRVVKADCSKNYAVAPEAVTEAISVDLSSGLIPFFICATVGTTS
          LVVYASDQ.H...QK...I.GI.P.NFRV........Y....E.V..A...DL.SGL.P...CATVGTT.
Retrocopy LVVYASDQSHTTFQKGARIVGIPPSNFRVIPTSAASSYGLTAESVRDAVEADLASGLVPLYLCATVGTTG

Parental  SSAVDPLPELGNIAQGHDMWFHIDAAYAGSACICPEYRHHLDGVEKADSFNMNAHKWFLTNFDCSLLWVK
          ..AVDP..ELG..A....MW.H.DAAYAGSA.ICPE......G.E.ADS..MN.HKWFLTN.DC..LWV.
Retrocopy VGAVDPVGELGEVARRYGMWLHVDAAYAGSALICPEFQGYMEGAELADSVSMNPHKWFLTNMDCCCLWVA

Parental  DRSYL
          ..S.L
Retrocopy TPSQL

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_50 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN539459.1_FG006	1 retrocopy	retro_olon_8,
Hordeum vulgare	MLOC_77509	1 retrocopy	retro_hvul_50 ,