RetrogeneDB ID: retro_hvul_103

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: morex_contig_50049:7871..8463(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_44559
• Aliases: None
• Description: None

Sequence

>retro_hvul_103
ATGGGCGAGCGGAAGGTGCTCAACAAACACTACCCGAACGACTTCGACCCGGCCAAGATCCCGCGGCGGCTGAAGCCCAA
GAACCAGCAGATCAAGGTGCGCATGATGCTCCAGATGAGCATCCGCTGCAGCACCTGCGGGACGTACATGGCCATGGGCA
CCAAGCTCAACTCGCGCAAAGAGGACGCCGCCGGCGAGGCATACCTGGGCATACGATACACCGGTTCTACATCAGGTGCA
CACGCTGCTCCGCCGAGATCACCTTCAAGACGGACCCCCGGAACTCGGACTACGCAGTGGAGTCGAGGGCAGCCGCAACT
TCGAGCCATGGCGCGAGGCTGAGGCTGTGGTGGACAAGGAGACGAGGAAGCGAGCGGCGGAGGAGATGGGCGATGCGATG
ACAGCCCTGGAGAACAGGGCCATGGGTTCCAAGCGGAACATGGACATATTTGCTGATTTGGAAGAGACGCGGTCGATCAG
GTCTAGGCATGACCGAGTCTCAACTGACCGGATGCTTGAGATTCTGAACCATTCTTCTTCTACTGCTCATCATCAAAATC
TAAATTTAAATGAAGAAAATACAGTACTACTA

Alignment

ORF - retro_hvul_103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.64 %
• Parental protein coverage: 56.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGERKVLNKYYPPDFDPAKIPRRKQPKNQQIKVRMMLPMSIRCGTCGTYIYKGTKFNSRKEDCIGETYLG
          MGERKVLNK.YP.DFDPAKIPRR..PKNQQIKVRMML.MSIRC.TCGTY...GTK.NSRKED..GE.YLG
Retrocopy MGERKVLNKHYPNDFDPAKIPRRLKPKNQQIKVRMMLQMSIRCSTCGTYMAMGTKLNSRKEDAAGEAYLG

Parental  IQ-IFRFYFKCTRCSAEITFKTDPQNSDYTVESGA-SRNFEPWREEDEVVDKEKRKREAEEMGDAMRALE
          I..I.RFY..CTRCSAEITFKTDP.NSDY.VES.A.SRNFEPWRE...VVDKE.RKR.AEEMGDAM.ALE
Retrocopy IR<IHRFYIRCTRCSAEITFKTDPRNSDYAVESRA<SRNFEPWREAEAVVDKETRKRAAEEMGDAMTALE

Parental  NRAMDSKQDMDILAALEEMRSMKSRHAGVSVDQMLEILKHSAHQKEEKTVAELDEEDEELI
          NRAM.SK..MDI.A.LEE.RS..SRH..VS.D.MLEIL.HS...........L.EE...L.
Retrocopy NRAMGSKRNMDIFADLEETRSIRSRHDRVSTDRMLEILNHSSSTAHHQNL-NLNEENTVLL

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_103 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_28326	1 retrocopy	retro_atau_32,
Hordeum vulgare	MLOC_44559	1 retrocopy	retro_hvul_103 ,
Medicago truncatula	MTR_2g070740	1 retrocopy	retro_mtru_38,