RetrogeneDB ID: retro_hvul_37

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 1:123895554..123896049(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_37956
• Aliases: None
• Description: None

Sequence

>retro_hvul_37
ATGCGGCCTGGAGTGAAATGGATCGACATGCACAAGCTGGCAGAGCGGAGAATACTCGAGTCTCTAAAGGAAGATAACAT
CATCCATGGCGATGTTGATGACATGATGAACGCAAGGTTGGGTGCCGTTTTCATGCCTCGTGGCCTTGGGCACTTGCTTG
GAATCGACGCCCATGATCCCGGAGGCTACCCTGAGGGTTTAGAGAAGCCAAAGGAGCCAGGGTTGGAGGCCTTGCGGACC
ACAAGAGAGCTTAAACAAGGCATGGTTATCACGGTCGAGCCAGGATGTTATTTCAGTGACTCTCTGCTGATGCGTGCGAG
GGATGATCCAGTTTGCTCAAAGTTCTTCGACTGGGAAACGATAGAAACGTACAAAAGCTTTGGTGGTGTTCGCATTGAAA
GTAATCTGTATGTGACGGCACAAGGGTGCAAGAACCTCACAAACTGCCCTCGAGAGATCTGGGAAATTGAAGCGGTAATG
GCTGGCATGCCATGG

Alignment

ORF - retro_hvul_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 91.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQPGVKWIDMHKLAEQTILESLKKEKIIHGDIADMMARRLGAVFMPHGLGHLLGIDTHDPGGYPEGLERP
          M.PGVKWIDMHKLAE..ILESLK...IIHGD..DMM..RLGAVFMP.GLGHLLGID.HDPGGYPEGLE.P
Retrocopy MRPGVKWIDMHKLAERRILESLKEDNIIHGDVDDMMNARLGAVFMPRGLGHLLGIDAHDPGGYPEGLEKP

Parental  NEPGLSSLRTIRELKEGMVITVEPGCYFIDALLRPARDDPISSKFFNWEEIEKYKSFGGVRIESDLYVTG
          .EPGL..LRT.RELK.GMVITVEPGCYF.D.LL..ARDDP..SKFF.WE.IE.YKSFGGVRIES.LYVT.
Retrocopy KEPGLEALRTTRELKQGMVITVEPGCYFSDSLLMRARDDPVCSKFFDWETIETYKSFGGVRIESNLYVTA

Parental  QGCKNLTNCPREIWEIEAVMAGAPW
          QGCKNLTNCPREIWEIEAVMAG.PW
Retrocopy QGCKNLTNCPREIWEIEAVMAGMPW

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_37 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_28657	1 retrocopy	retro_atau_71,
Hordeum vulgare	MLOC_37956	1 retrocopy	retro_hvul_37 ,