RetrogeneDB ID: retro_hvul_7

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 2:610515033..610516110(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_20759
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_16373
• Aliases: None
• Description: None

Sequence

>retro_hvul_7
ATGGCACTCCGAAGGCTGCTTCAGGGGGCCGTTCTACCGAGGACGATGGGACGGTCCTTGTCCACTGCGCCCGGGGAGGC
TATCCGCGCAACCCTCTTCCCCGGCGACGGCATCGGGCCGGAGATCGCCGAGTCGGTGAAGCAGGTGATCAACGTTGCAG
GCGTGCCAATAGAATGGGAAGAGCATTATGTCGGCGCGGAGGTTGATCCCAGAACACAGAGCTTCTTGACATGGGAAAGC
CTGGAGTCGGTGCGCAGAAACAAGGTTGGCCTGAAAGGCCCTATGGCCACACCCATTGGAAAAGGCCACCGTTCTCTGAA
TCTCACACTGAGGAAAGAGCTCGGGCTCTACGCCAATGTCAGACCTTGCAACAGCCTCCCGGGCTACAAGACCAGATACG
ACGACGTGAACCTCGTGACCATCCGCGAGAACACGGAAGGGGAGTACAGCGGCCTCGAGCACCAGGTCGTCAGGGGCGTC
GTGGAAAGCCTCAAGATCATCACCCGCCAGGCTAGCCTGAGGGTGGCGGAGTACGCTTTCCATTACGCCAAGGCCAATGG
CAGGGAGAGGGTCTCGGCGATACACAAGGCCAACATCATGAGGAAGACAGACGGGCTTTTCCTCCAGTGCTGCCGCGAGG
TGGCCGCCAAGTACCCTGAGATCAAGTACGAGGAGGTGGTCATCGACAACTGCTGCATGGAGCTCGTCAAGGACCCTGGC
ACGTATGATGTGCTGGTGATGCCCAACCTGTACGGCGACATTATCAGTGATCTGTCCGCCGGTTTGATCGGGGGCCTGGG
CTTGACTCCCAGCTGCAACATTGGTGAGGGCGGCATCTGTCTGGCGGAGGCTGTTCATGGCTCTGCACCTGATATCTCTG
GCAAGAACCTTGCAAACCCAACTGCTCTTATGCTCAGTGCTGTTATGATGCTGCGCCACCTGCATTTCAACAACCAGGCA
GACCGGATCCACAATGCCATCCTACGCACCATCGCCGACGGCAAGTACAGGACCGCTGATCTTGGTGGCAAGTCGTCGAC
ATCGGACTACACAAAAGCAGTCTGCGATCATATCTGA

Alignment

ORF - retro_hvul_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATPIGKGHRSLNLTLRKELGLYANVRPCNSLPGYKTRYDDVNLVTIRENTEGEYSGLEHQVVRGVVESL
          MATPIGKGHRSLNLTLRKELGLYANVRPCNSLPGYKTRYDDVNLVTIRENTEGEYSGLEHQVVRGVVESL
Retrocopy MATPIGKGHRSLNLTLRKELGLYANVRPCNSLPGYKTRYDDVNLVTIRENTEGEYSGLEHQVVRGVVESL

Parental  KIITRQASLRVAEYAFHYAKTNGRERVSAIHKANIMRKTDGLFLKCCREVAEKYPEITYEEVIIDNCCMT
          KIITRQASLRVAEYAFHYAK.NGRERVSAIHKANIMRKTDGLFL.CCREVA.KYPEI.YEEV.IDNCCM.
Retrocopy KIITRQASLRVAEYAFHYAKANGRERVSAIHKANIMRKTDGLFLQCCREVAAKYPEIKYEEVVIDNCCME

Parental  LVKNPGTFDVLVMPNLYGDIISDLCAGLIGGLGLTPSCNIGEGGICLAEAVHG
          LVK.PGT.DVLVMPNLYGDIISDL.AGLIGGLGLTPSCNIGEGGICLAEAVHG
Retrocopy LVKDPGTYDVLVMPNLYGDIISDLSAGLIGGLGLTPSCNIGEGGICLAEAVHG

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_7 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
Aegilops tauschii	F775_26510	1 retrocopy	retro_atau_46,
Hordeum vulgare	MLOC_16373	1 retrocopy	retro_hvul_7 ,