RetrogeneDB ID: retro_hvul_90

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:54495462..54496308(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_4579
• Aliases: None
• Description: None

Sequence

>retro_hvul_90
GCCGTCGGGCATGGGATCGAGCCGGACCTCCTGGGCGAGATGATGGCGGTGACGAGGGAGTTCTTCAACCTCCCGCTGGA
AGAGAAGCAGAGGTACACCAACCTGGTCGGCGGCAAGAAGGAGTACAGGATCGAGGGCTACGGCGGCGACATGGTCCTGT
CGGAGACCCAGGTCCTGGACTGGTGCGACCGGTTCTACCTCGTCGTGTACCCGGAGTCGCGGCGCCTCCACGACCTCTGG
CCGACGCGGCCCCCCTCCTTCCGGGACGTCCTGCACCGGTACTCCGCGCGGTGCAGGGAGCTCGCCGACGCCGTGCTTCG
GGAGGCAGCCGGCGCGGCGGGGCTCCCCGACGAGGGGTACCTGGCCGACATGCTCGACGAGAAGGCCGTGACCTACGTGC
GGCTCAACTGCTACCCCCCATGCCCGCGCCCCGACCGCGTGCTCGGGTTCAGGCCCCACTCCGACGGCGGCGCGCTCACC
GTCCTGCTCGCCGAAACCGCCGGGCTCCAGGTGCGCCGTGACAGCGACGGAGGCGGCGGTGAATGGTACGACGTGCCCGT
GGTGCCCGGCGCGCTGGTGGTGAATTTGGGGGACACGGTGGAGGTGGTGAGCAACGGGGTGCTGAGGAGCCCGGTGCACA
GGGTGGTGGCGAGCGGTGAGAGGGAGCGGGTGTCGGTGGCGGCGTTCTACACGGTGGACCCGGAGAGGGAGGTGGAGCCG
GCTCCGGAGCTGGTGAGCGAGGAGAGGCCCAGGCGGTACGAGAAGACCAAGAAGGCCGGCGACTACGTCAGGGAGCTGCT
GGAGAGCTTGGCGCGAGGGGAGAGGGCCATCGACAGGGTGAAGCTC

Alignment

ORF - retro_hvul_90 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.26 %
• Parental protein coverage: 77.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVGHGMEQSFLGEVMKVAREFFKLPLEEKQKYSNLVNGD-EVRIEGYGNDMVVSEKQILDWCDRLYIIVE
          AVGHG.E...LGE.M.V.REFF.LPLEEKQ.Y.NLV.G..E.RIEGYG.DMV.SE.Q.LDWCDR.Y..V.
Retrocopy AVGHGIEPDLLGEMMAVTREFFNLPLEEKQRYTNLVGGKKEYRIEGYGGDMVLSETQVLDWCDRFYLVVY

Parental  PENRRIYSLWPTQPPSFRDILSEYTVRCHKIANLFLQNLAKLLDL-HEDYFVNMFDENALTYARLNYYPN
          PE.RR...LWPT.PPSFRD.L..Y..RC...A...L...A....L..E.Y...M.DE.A.TY.RLN.YP.
Retrocopy PESRRLHDLWPTRPPSFRDVLHRYSARCRELADAVLREAAGAAGLPDEGYLADMLDEKAVTYVRLNCYPP

Parental  CPKPDHVFGMKPHTDASVITIVFIDDNVSGLQLQND---GVWYNVPIVPNALLVNVGDVMEIMSNGFFKS
          CP.PD.V.G..PH.D....T...............D...G.WY.VP.VP.AL.VN.GD..E..SNG...S
Retrocopy CPRPDRVLGFRPHSDGGALTVLLAETAGLQVRRDSDGGGGEWYDVPVVPGALVVNLGDTVEVVSNGVLRS

Parental  PIHRVVTNAEKERLSLVMFYTMNPEKEIEPLPELVDEKRPRRYRKT-TTNDYIAKLFETFARGTLAIDTV
          P.HRVV...E.ER.S...FYT..PE.E.EP.PELV.E.RPRRY.KT....DY...L.E..ARG..AID.V
Retrocopy PVHRVVASGERERVSVAAFYTVDPEREVEPAPELVSEERPRRYEKTKKAGDYVRELLESLARGERAIDRV

Parental  KI
          K.
Retrocopy KL

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_90 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_4579	1 retrocopy	retro_hvul_90 ,
Hordeum vulgare	MLOC_36995	1 retrocopy	retro_hvul_91,