RetrogeneDB ID: retro_hvul_18

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 4:265271872..265272955(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_21639
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_76287
• Aliases: None
• Description: None

Sequence

>retro_hvul_18
ATGGAGTCCATCACCGCCAGCACCACCCTGCTCAAGTTCACCTACGACGACATCAAGATGGCCACGGGGAGCTTCGCTAG
AGACAGCATCATCGGCCGCGGTGGCTTCGGGAATGTCTACAAGGGGGTGCTCCCAGATGGCGCGGAGGTGGCAGTGAAAC
GCTTCAAGAACTGCTCGGCAGCCGGGGATGCCGCGTTCGCACATGAGGTGGAGGTGGTGGCCAGCGTGCGCCATGTCAAC
CTGGTTGCGCTCCGTGGCTACTGCATCGCCGCCACGCAGAGAGAGGGGCACCAGCGGATGATTGTGTGCGACCTCATGCA
TAATGGCAGCCTCCACGACCACCTCTTCGGCGCCGGGGAGTGCCTGATGGCATGGCCAGTGAGGCAGAGGATTGCCATCG
GGATGGCACGGGGGCTGTCCTACCTGCACCGTGGCACACAGCCAGCTATCATTCACAGGGACATCAAGGCAAGCAACATC
TTGCTCGATGATGATTTTGAGGCAAAGGTGGCCGATTTTGGATTGGCCAAGTTTGCACCCGAAGGGATGACACACGTGAG
CACACGGGTTGCTGGCACAATGGGCTATGTCGCTCCAGAGTATGCCCTCTATGGCCAGTTAACTGAGAAGAGTGATGTCT
ACAGCTTCGGAGTTGTTCTTCTTGAGCTTCTGAGTGGGAAGAGAGCATTCATGTCTCTCAATGAGGGAGAGAGCTTCGTG
CTTGCTGACTGGGCTTGGTCATTGGTTCGGAGGGGGAAGACGCTGGATGTGCTCCAGGAAGGAATGGCTGAACCTGGTCC
TACTAAGGTCATGGAGAAGTATGTACTTGTGGCAGCACTCTGCACACATCCACAGCTGCATGCCAGGCCAACAATGGAGC
AAGCGGTGAAGATACTAGAAGCAGATTCAGCACCAGGGCCGTTAATCATTCCGGACAGGCCTCTCCCTGTTGTTGCAAAC
CTGGCCGAGATTGAGAGGTCAGTGAGCAGCACCGGCTCAGGTCAGCTGTTCAGTCCCTCTGGTTTCCGGTCTTTTATTCA
TAGAAACGAGGATGCTACACGGGAATCTCCAAAAGAAACATGA

Alignment

ORF - retro_hvul_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.17 %
• Parental protein coverage: 54.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTYEELGAATGGFSKANLLGQGGFGYVYKGVLPGSGKEVAVKQLKAGSGQGEREFQAEVEIISRVHHRHL
          FTY.....ATG.F......G.GGFG.VYKGVLP..G.EVAVK..K..S..G...F..EVE....V.H..L
Retrocopy FTYDDIKMATGSFARDSIIGRGGFGNVYKGVLP-DGAEVAVKRFKNCSAAGDAAFAHEVEVVASVRHVNL

Parental  VSLVGYCIAGSS----QRLLVYEFVANDTLERHLHGNGVPVMDWPKRLSIALGSAKGLAYLHEDCNPRII
          V.L.GYCIA.......QR..V.....N..L..HL.G.G...M.WP.R..IA.G.A.GL.YLH....P.II
Retrocopy VALRGYCIAATQREGHQRMIVCDLMHNGSLHDHLFGAGECLMAWPVRQRIAIGMARGLSYLHRGTQPAII

Parental  HRDIKAANILLDENFEAKVADFGLAKLTTDNNTHVSTRVMGTFGYLAPEYASSGKLTDKSDVFSFGVMML
          HRDIKA.NILLD..FEAKVADFGLAK......THVSTRV.GT.GY.APEYA..G.LT.KSDV.SFGV..L
Retrocopy HRDIKASNILLDDDFEAKVADFGLAKFAPEGMTHVSTRVAGTMGYVAPEYALYGQLTEKSDVYSFGVVLL

Parental  ELITGRRPVDPTNYMED-SLVDWARPLLAR
          EL..G.R.....N..E...L.DWA..L..R
Retrocopy ELLSGKRAFMSLNEGESFVLADWAWSLVRR

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_18 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_54206	1 retrocopy	retro_hvul_99,
Hordeum vulgare	MLOC_76287	1 retrocopy	retro_hvul_18 ,