RetrogeneDB ID: retro_hvul_86

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 6:509465310..509465865(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_5075
• Aliases: None
• Description: None

Sequence

>retro_hvul_86
ATGCAGGAGGGGCTCGCCCACCTGTTCCTCGTCGGGCGGAGCGTCACGGCCACCAGGGCGCGCGTCGAGGTGCCCATCCC
CAGGAAGCATGGGCACGGCTCCGGCGCCTACGACGCCGCCCTCAGGGACTTCTTCCAGCGCGTCCTGGCCGCCTTCGTGC
ACCACGTCGACTTCGGCCTCGTCCAGTGCGTGGTGATCGCCAGCCCGGGCTTCACCAAGGAGCAGTTCCGCGACCACATG
CTCCTGGAGGCCGCGCGGCGAGGGGAGCTGCGCGCCATCACGGACCACAAGGCGCGCATCGCGCTCGCGCCCGCCACCTC
GGGCTACCCGCACAGCCTCAAGGACGTCCTCGCCGCCCCGGGCGTCATGTCGCTGGTGAAGGACACGAGGGCGGCGCAGG
AGGTGCCGGCGCTGCAGGAGTTCTTCGCCATGATCGCCAAGGACTCGGCGCGGGCCTGCTACGGGCCCAAGCACGTCGAG
GTCGCGCACGAACGCCTCGCCATCCAGACCCTCCTGCTCACGGACACCTGGTTCCGGAACCCCGACGTTGCTGCT

Alignment

ORF - retro_hvul_86 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.81 %
• Parental protein coverage: 95.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQEGLAHLFLIGRSITATRSRIETSIPRKHGPAIAGYESALKKFFEHVLQALLKHIDFEVVQCVVIASPG
          MQEGLAHLFL.GRS.TATR.R.E..IPRKHG.....Y..AL..FF..VL.A...H.DF..VQCVVIASPG
Retrocopy MQEGLAHLFLVGRSVTATRARVEVPIPRKHGHGSGAYDAALRDFFQRVLAAFVHHVDFGLVQCVVIASPG

Parental  FTKDQFRDYMHLEAARR-DLRVIIENKSRIILAHAPSGYKHSLKEVLDTPGVMSLIKDTKAAQEVQALKE
          FTK.QFRD.M.LEAARR..LR.I...K.RI.LA.A.SGY.HSLK.VL..PGVMSL.KDT.AAQEV.AL.E
Retrocopy FTKEQFRDHMLLEAARRGELRAITDHKARIALAPATSGYPHSLKDVLAAPGVMSLVKDTRAAQEVPALQE

Parental  FFAMLTNDSARACYGPKHVEVAHERLAIQTLLMTDTLFRNTNIAS
          FFAM...DSARACYGPKHVEVAHERLAIQTLL.TDT.FRN...A.
Retrocopy FFAMIAKDSARACYGPKHVEVAHERLAIQTLLLTDTWFRNPDVAA

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_86 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT4G27650	1 retrocopy	retro_atha_7,
Brassica oleracea	Bo7g111550	1 retrocopy	retro_bole_15,
Brassica rapa	Bra019037	1 retrocopy	retro_brap_29,
Aegilops tauschii	F775_08238	1 retrocopy	retro_atau_9,
Hordeum vulgare	MLOC_5075	1 retrocopy	retro_hvul_86 ,
Theobroma cacao	TCM_025327	1 retrocopy	retro_tcac_21,
Vitis vinifera	VIT_04s0023g00140	1 retrocopy	retro_vvin_2,