RetrogeneDB ID: retro_hvul_9

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 6:201138119..201138800(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_74367
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_12954
• Aliases: None
• Description: None

Sequence

>retro_hvul_9
ATGGCCACCGCGTCGCTGTCCGCTCTGTCCTCGTCGGCCGCCGCCGCCGGCAGGCGCTTCGTCCTCTCCTCCCCGTCGCT
CGCCTTCGCCTCCCGCCGCATCGCCGCCCCAGCCCGCCTCCGCGCCGCCGTTCTTCCGGGGGAAAGGAGATTCGCGGCGT
CCGCGGCATCGGCATCCCCGGTCGTGGCCACCATCGCGGTCGGCGACAAGCTGCCCGACGCCACGCTCTCCTACTTCGAC
CCAGCCGACGGCGAGCTGAAGACGGTGACGGTCGGCGACCTCACGGCGGGGAAGAAGGTCGTGCTCTTCGCTGTCCCGGG
CGCCTTCACCCCGACCTGCTCGCAGAAGCACCTGCCGGGGTTCGTCGAGAAGGCGGGCGAGCTGCGCGCCAAGGGGGTGG
ACACCGTGGCGTGCGTCTCGGTGAACGACGCCTTCGTGATGAAGGCGTGGAAGGAGAGCCTCGGCCTCGGCGACGACGTG
CTGCTGCTGTCGGACGGCAACCTCGAGCTCACCCGCGCGCTGGGCGTGGAGATGGACCTCTCCGACAAGCCCATGGGGCT
AGGCGTGCGGTCCCGCCGCTACGCGCTCCTCGCAGACGACGGCGTCGTCAAGGTGCTCAACCTCGAGGAGGGCGGCGCCT
TCACCACCAGCAGCGCCGAGGAGATGCTCAATGCGCTCTGA

Alignment

ORF - retro_hvul_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.03 %
• Parental protein coverage: 76.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARATMAPIGVGSTLPDGQLGWFDEND-QLQQVSIHSLAAGKKVILFGVPGAFTPTCSNQHVPGFITQAED
          A....A.I.VG..LPD..L..FD..D..L..V....L.AGKKV.LF.VPGAFTPTCS..H.PGF...A..
Retrocopy ASPVVATIAVGDKLPDATLSYFDPADGELKTVTVGDLTAGKKVVLFAVPGAFTPTCSQKHLPGFVEKAGE

Parental  LKAKGVEEILLVSVNDPFVMKAWAKTYPENKHVKFLADGAAAYTKALGLELDLTEK--GLGLRSKRFALL
          L.AKGV.....VSVND.FVMKAW.........V..L.DG....T.ALG.E.DL..K..GLG.RS.R.ALL
Retrocopy LRAKGVDTVACVSVNDAFVMKAWKESLGLGDDVLLLSDGNLELTRALGVEMDLSDKPMGLGVRSRRYALL

Parental  ADDLKVTVANIEEGGQFTISGAEEILKAL
          ADD..V.V.N.EEGG.FT.S.AEE.L.AL
Retrocopy ADDGVVKVLNLEEGGAFTTSSAEEMLNAL

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_9 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G65980	1 retrocopy	retro_atha_13,
Arabidopsis lyrata	fgenesh2_kg.2__836__AT1G65980.1	1 retrocopy	retro_alyr_5,
Glycine max	GLYMA07G09240	1 retrocopy	retro_gmax_12,
Hordeum vulgare	MLOC_12954	1 retrocopy	retro_hvul_9 ,
Populus trichocarpa	POPTR_0018s09030	1 retrocopy	retro_ptri_12,
Prunus persica	PRUPE_ppa012586mg	1 retrocopy	retro_pper_22,
Sorghum bicolor	Sb03g030950	1 retrocopy	retro_sbic_22,
Selaginella moellendorffii	SELMODRAFT_159225	1 retrocopy	retro_smoe_4,
Solanum lycopersicum	Solyc07g020860.2	1 retrocopy	retro_slyc_41,
Theobroma cacao	TCM_028816	1 retrocopy	retro_tcac_8,