RetrogeneDB ID: retro_hvul_30

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:36974182..36975319(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_57678
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_65304
• Aliases: None
• Description: None

Sequence

>retro_hvul_30
ATGGCTCGGCGAATCAATGGCGTCACTGCCGCCGCCTCCGCCAGCCTCCTCCTCGCCTTCCTCATGCCGGCTGCCGCGGA
CGGCGACGGCGGCGGGACAACGCGGTACAACGCCATGTTCAACTTCGGTGACTCGCTGTCGGACACGGGCAACCTCTGCG
TGAACAAGTCGGCGGCGGCGGAGCTCCTGCTCACCTTCGCCAACCCGCCCTACGGCATGACCTACTTCGGCCGCCCCACC
TGCCGCTGCTCCGACGGCCGGCTCGTCGTCGATTTCCTCGCGCAGTCGCTGGGCCTCCCTTTCCTTCCCCCGTCCAAGCT
CCCCGGCGCCGACTTCCGGAAGGGCGCCAACATGGCCATCATCGGCGGCACGGCGCTCGACTTCGAGTTCCTCAAGTCCA
TCGGCCTCGGCTACCCGATCTGGAACAACGGCGCCATCAACGTGCAGCTCCGGTGGTTCCGCGACCTGCTCCCGCGCGTC
TGCGGCGGGCCGCAGACCTGCAGGCCCTACCTCGCCAGGTCCCTCTTCCTCCTCGGCTCCATCGGCGGCAACGACTACAA
CGCCATGCTCTTCTTCGGCTTCAACGTCAGCCGGGCCAAGAGCTACGCCCCCAACGTGGTCGACAACATCGCCGCCGCCG
TCGAGAGGCTGATCGAGCTGGGCGCGGCGGACATCGTGGTGCCGGGCACGCTCCCCATCGGGTGCATCGCCGTCTACCTC
GCCATCCTCCCGAGCGGCGACAAGTCCGACTACGACGAGCGCGGCTGCCTCAAGCCGCTCAACGGCCTCGCCATGTACCA
CAACTCGCTGCTCCAGGACAGGCTCAACGGCGTCCGCGCCAGGCATGGCTCGGCGGTGAGGATCATGTACGCGGACTACT
ACGCCCACGCCGTCGACATGCTCCGTGACCCGGCGCGCTTCGGCTTCACCACGGTGATCACGGCGTGCTGCGGCGCGGGC
GGCGGCCCGTACAACTACGAGTTCGACGCGCGGTGCGGGATGAAGGGCGCGACCGCGTGTGCCGACCCGTGGAGGCATGA
GTCATGGGACGGCGTGCATCCGACGGAGGCGGTGAACAAGCTCGTCGCCGACGGGTGGCTCAGGGGACCATACTGTCACC
CTCCCATCCTGCAGTAA

Alignment

ORF - retro_hvul_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.6 %
• Parental protein coverage: 91.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KYNAVYSFGDSITDTGNLCTNGRPSA---ITFTQPPYGETYFGSPTCRCSDGRVIVDFLSTKYGLPFLPP
          .YNA...FGDS..DTGNLC.N....A....TF..PPYG.TYFG.PTCRCSDGR..VDFL....GLPFLPP
Retrocopy RYNAMFNFGDSLSDTGNLCVNKSAAAELLLTFANPPYGMTYFGRPTCRCSDGRLVVDFLAQSLGLPFLPP

Parental  SKSTSADFKKGANMAITGATAMDAPFFRSLGLSDKIWNNGPISFQLQWFQTITSSVCGS--SCKSYLANS
          SK...ADF.KGANMAI.G.TA.D..F..S.GL...IWNNG.I..QL.WF......VCG....C..YLA.S
Retrocopy SKLPGADFRKGANMAIIGGTALDFEFLKSIGLGYPIWNNGAINVQLRWFRDLLPRVCGGPQTCRPYLARS

Parental  LFIFGEFGGNDYNAMLFGNYNTDQASTYAPQIVDTISAGVEKLVAMGATDVVVPGVLPIGCFPIYLTIYG
          LF..G..GGNDYNAMLF...N...A..YAP..VD.I.A.VE.L...GA.D.VVPG.LPIGC...YL.I..
Retrocopy LFLLGSIGGNDYNAMLFFGFNVSRAKSYAPNVVDNIAAAVERLIELGAADIVVPGTLPIGCIAVYLAILP

Parental  TSSAADYDSLGCLKKFNDLSTYHNSLLQAKVSTLQAKYKSA-RIMYADFYAGVYDMVRSPSKYGFSSVFE
          .....DYD..GCLK..N.L..YHNSLLQ.......A...SA.RIMYAD.YA...DM.R.P...GF..V..
Retrocopy SGDKSDYDERGCLKPLNGLAMYHNSLLQDRLNGVRARHGSAVRIMYADYYAHAVDMLRDPARFGFTTVIT

Parental  ACCGSGGGKYNYANSARCGMSGASACASPASHLSWDGIHLTEAAYKQITDGWLNGAFCHPAI
          ACCG.GGG.YNY...ARCGM.GA.ACA.P..H.SWDG.H.TEA..K...DGWL.G..CHP.I
Retrocopy ACCGAGGGPYNYEFDARCGMKGATACADPWRHESWDGVHPTEAVNKLVADGWLRGPYCHPPI

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_30 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_65304	1 retrocopy	retro_hvul_30 ,