RetrogeneDB ID: retro_hvul_99

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:575955952..575956831(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_54206
• Aliases: None
• Description: None

Sequence

>retro_hvul_99
ATCTACAGCTACAAGGAGCTCCACGCGGCCACGGGCGGCTTCAGCGAGGAGAACAAGCTGGGCGAGGGCGGCTTCGGCAG
CGTCTACTGGGGCAAGACCCCCGACGGCGTCCAGATCGCCGTCAAGCGCCTCAAGCCCAACAACAACAACTCCAAGGCCG
AGATGGAGTTCGCCGTCGAGGTCGAGGTGCTCGCCCGCGTCCGCCACCGCAACCTGCTCGGCCTCCGCGGCTACTGCGCC
GGCGCCGCCGCCGACCAGCGCATGATCGTGTACGACTACATGCCCAACCTCAGCCTCCTCTCGCACCTCCACGGCCAGTT
CGCCTCCGACGCCACCCTCGACTGGCGCCGCCGCGTGGGCGTGGCCGTCGGCGCCGCCGAGGCGCTCGTGCACCTCCACC
ACGAGGCGTCGCCCAGCATCATCCACCGCGACATCAAGGCCAGCAACGTGCTGCTTGACTCCGACTTCGCGCCGCTCGTC
GCTGATTTCGGGTTCGCCAAGCTCGTCCCCGACGGCGTCTCCCACATGACCACCAGGGTCAAGGGCACCCTCGGCTACCT
CGCGCCGGAGTACGCCATGTGGGGCAAGGTCTCCGGGGCGTGCGACGTGTACAGCTTCGGCATTCTGCTCGTGGAGCTCG
TCTCCGGCAGGAAGCCCATCGAGCGGCTGCCGTCGGGTGCCAAGCGCACCATCACCGAGTGGGCGGAGCCGCTCATCGCA
CGCGGCCGGCTCGGGGACCTCGTGGACCCGCGCCTCCGGGGCGTCTACGACGCGGCGGAGCTGGCGCGCATGCTCGAGGC
CGCCGCGCTCTGCGTGCAGGGGGAGCCCGAGCGGCGCCCGGACATGCGCGCCGTCGTGCGGATCCTGCGCGGCGAGACC

Alignment

ORF - retro_hvul_99 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.88 %
• Parental protein coverage: 78.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFSLRELRSATNSFNYDNKIGEGSLGSVYWGQVWDGSQIAVKKLK--NARNGAEMEFAAEVESLGRVRHK
          ..S..EL..AT..F...NK.GEG..GSVYWG...DG.QIAVK.LK..N....AEMEFA.EVE.L.RVRH.
Retrocopy IYSYKELHAATGGFSEENKLGEGGFGSVYWGKTPDGVQIAVKRLKPNNNNSKAEMEFAVEVEVLARVRHR

Parental  NLLSLRGYCADGP--ERILVYDYMPNSSLFAHLHGTHSSECLLDWRRRTFIAIGAARALAYLHHHATSPI
          NLL.LRGYCA......R..VYDYMPN.SL..HLHG...S...LDWRRR...A.GAA.AL..LHH.A...I
Retrocopy NLLGLRGYCAGAAADQRMIVYDYMPNLSLLSHLHGQFASDATLDWRRRVGVAVGAAEALVHLHHEASPSI

Parental  IHGSIKSTNVLLDSDFQAHVGDFGLMKLISDEIDHDKIIGENQRGYHAPEYVMFGKPTTGCDVYSFGIIL
          IH..IK..NVLLDSDF...V.DFG..KL..D...H.........GY.APEY.M.GK....CDVYSFGI.L
Retrocopy IHRDIKASNVLLDSDFAPLVADFGFAKLVPDGVSHMTTRVKGTLGYLAPEYAMWGKVSGACDVYSFGILL

Parental  LELTSGRKPVEKSGSQKMLGVRNWMLPLAKEGRYDEIADSKLNDKYSESELKRVVLIGLACTHREPEKRP
          .EL.SGRKP.E...S........W..PL...GR.....D..L...Y...EL.R.......C...EPE.RP
Retrocopy VELVSGRKPIERLPSGAKRTITEWAEPLIARGRLGDLVDPRLRGVYDAAELARMLEAAALCVQGEPERRP

Parental  TMLEVVSLLKGES
          .M..VV..L.GE.
Retrocopy DMRAVVRILRGET

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_99 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,