RetrogeneDB ID: retro_hvul_16

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:361548463..361549258(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_77966
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_56081
• Aliases: None
• Description: None

Sequence

>retro_hvul_16
ATGGAGGACGCCGTCTCCATACGGGAGGCCTTCACCGTCCCGGCCGAGGAGGGGAAACCCGGGCGCGACTTCTACGGCGT
TTTCGACGGGCACGGCTGCTCCCACGTGGCGGACGCGTGCCGGGAGCGGATGCATGAGCTCGTTGCCGAGGAGCTGGCCG
GCGCGGCCCGGCCCGAGTCCTGGACCGCCGCAATGGTGCGCAGCTTCGCGAGGATGGACGCCGAGGTGACAGCCGGCGGG
GGCGGCGACAGCGCCAGCTGCCGGTGCGAGGTGAACAAGTGCGACCACGTGGGGTCCACGGCCGTGGTGGCCGTAGTGGA
GGAGCAGCGCGTCCTGGTGGCCAACTGCGGCGACTCCCGCGCCGTGCTCTGCCGCGACGGCGCGCCCGTCGTCCTCTCCT
CCGACCACAAGCCCGACAGGCCGGACGAGCTGGAGAGGATCGAGGCGGCCGGCGGCCGCGTCATATTCTGGGAGGGCGCG
AGGGTGCTGGGCGTCCTGGCCATGTCGCGCGCCATCGGCGACGGCTACCTCAAGCCGTTCGTGACCGCCGTCCCGGAGGT
GACGGTGACAGACAGGGCGGCCGGCGACGAGTGCCTGATCCTGGCCAGCGACGGGCTGTGGGACGTGGTCAGCAACGAGA
CGGCGTGCCAGGTGGCGCGGGCCTGCCTCCGGAGGGGCAGAGAGAGGTGGTGCGCCGAGGCAGCCGCCATGCTCACCAAG
ATGGCTCTCACGAAGAACAGCTCGGACAACATCTCTGTTGTCGTCGTCGATCTCCGGCCAAAGAACCATTTATAG

Alignment

ORF - retro_hvul_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.27 %
• Parental protein coverage: 55. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGHHFFGVFDGHGCSHVATSCGERMHEIVADEARSSGSDDAERWTGVMERSFARMDAEAVGSRSRASGAE
          PG..F.GVFDGHGCSHVA..C.ERMHE.VA.E....G....E.WT..M.RSFARMDAE.........G..
Retrocopy PGRDFYGVFDGHGCSHVADACRERMHELVAEEL--AGAARPESWTAAMVRSFARMDAEV----TAGGGGD

Parental  AAPNCRCELQLPKCDHVGSTAVVAVVGPRHLIVANCGDSRAVICRGGAAIPLSSDHKPDRPDELERIQAA
          .A..CRCE....KCDHVGSTAVVAVV......VANCGDSRAV.CR.GA...LSSDHKPDRPDELERI.AA
Retrocopy SA-SCRCEVN--KCDHVGSTAVVAVVEEQRVLVANCGDSRAVLCRDGAPVVLSSDHKPDRPDELERIEAA

Parental  GGRVIFWDGARVFGVLAMSRAIGDSYLKPFVIPDPEVRVLERKDGEDEFLILASDGLWDVVSNEVACHVV
          GGRVIFW.GARV.GVLAMSRAIGD.YLKPFV...PEV.V..R..G.DE.LILASDGLWDVVSNE.AC.V.
Retrocopy GGRVIFWEGARVLGVLAMSRAIGDGYLKPFVTAVPEVTVTDRAAG-DECLILASDGLWDVVSNETACQVA

Parental  RSCVRSKAKR
          R.C.R....R
Retrocopy RACLRRGRER

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_16 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_56081	1 retrocopy	retro_hvul_16 ,
Oryza punctata	OPUNC03G11550	1 retrocopy	retro_opun_31,
Oryza sativa japonica	OS03G0268600	1 retrocopy	retro_osat_49,
Sorghum bicolor	Sb01g039890	1 retrocopy	retro_sbic_41,
Setaria italica	Si036015m.g	1 retrocopy	retro_sita_14,