RetrogeneDB ID: retro_hvul_36

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 1:36429388..36430699(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_54046
• Aliases: None
• Description: None

Sequence

>retro_hvul_36
GAATCTGAGGCGAAGCTCAAGGACGTGAACCTGGACGACTGGCTGCCCATCACCTCCTCGCGCACCGCCAAGTGGTACTA
CTCCGCCTTCCACAACGTGACGGCCATGGTCGGCGCCGGCGTGCTGGGCCTCCCGTTCGCCATGTCGCACCTCGGTTGGG
GCCCCGGCGTGGCCGTCATCGCCAGCTCCTTCGGGATCACGCTCTACACGCTGTGGCAAATGGTGGAGATGCACGAGATG
GTCCCGGGGAAGCGCTTCGACCGGTACCACGAGCTGGGGCAGCACGCCTTCGGGAAGAAGCTCGGGCTCTGGATCATCGT
CCCGCAGCAGCTCGTCGTCGACGTCGGCACCGACATCGTCTACATGGTCACCGGCGGCCAGTCGCTCAAGAAGTTCCACG
ACCTCGTCTGCAACGGCCGCTGCAGGGACATCCGCCTCACCTTCTTCATCATGATCTTCGGCTCCGTCCACTTTCTGCTC
TCCCAGATGCCCAACTTCAACTCCATCTCCGGCGTCTCCGCCGCCGCCGCCGTCATGTCCATCTGCTACTCCATGGTCGC
CTTCTTCGCGTCCGTGGTACACAAACACCCGGTCGGGGCCGCCGTCGTCGACTACGGGCTCAAGGCCACGAGCACCGCGG
GGCACGTGTTCGGCGCGTTCAACGCTCTCGGGGCGGTCGCCTTCGCCTTCGCCGGCCACAATGTCGTGCTCGAGATCCAG
GCCACCATCCCGTCCACACCGGAGCAGCCGTCCAAGAAGCCTATGTGGCGCGGCGTGATGGTCGCCTACGCCATCGTCGC
GCTCTGCTACTTCTCCGTCGCCTTCGGCGGGTACTACGCCTTCGGCAACTCCGTCGACCCCAACATCCTCATCACGCTCG
ACAAGCCACGGTGGCTCATCGCCATGGCCAACCTCATGGTCGTCGTCCATGTCATCGGCAGCTACCAGGTGTTCGCCATG
CCCGTGTTTGACATGATGGAGACCGTGCTCGTCAAGAAGCTCAAGTTCACCCCCGGCCTCCCGCTCCGGCTCACCGCCCG
CTCCGCCTACGTCGCGCTCACGATGCTCATCGGCATGACATTCCCCTTCTTCGACGGCCTGCTCGGCTTCTTCGGAGGCT
TCGCGTTCGCGCCCACCACCTACTTCCTACCCTGCATCATCTGGCTAATCCTGCGCAAGCCCGCCAGGTACAGCACTACA
TGGTTCCTCAACTGGATATTCATCGTCATCGGAGTCTTGCTCATGTTACTGTCCCCCATCGGCGGATTGCGCCAAATCAT
CCTCGACGCCAAGACTTTCAAGTTCTACTCT

Alignment

ORF - retro_hvul_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.77 %
• Parental protein coverage: 97.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDERTAREKAIDDWLPITSSRKAKWWYSAFHNVTAMVGAGVLSLPYAMSELGWGPGIAVMTLSWIITVYT
          ..E........DDWLPITSSR.AKW.YSAFHNVTAMVGAGVL.LP.AMS.LGWGPG.AV...S..IT.YT
Retrocopy ESEAKLKDVNLDDWLPITSSRTAKWYYSAFHNVTAMVGAGVLGLPFAMSHLGWGPGVAVIASSFGITLYT

Parental  LWQMVEMHEMVPGKRFDRYHELGQHAFGDKLGLWIVVPQQLVVEVSLNIVYMVTGGNSLKKFHDVICDGK
          LWQMVEMHEMVPGKRFDRYHELGQHAFG.KLGLWI.VPQQLVV.V...IVYMVTGG.SLKKFHD..C.G.
Retrocopy LWQMVEMHEMVPGKRFDRYHELGQHAFGKKLGLWIIVPQQLVVDVGTDIVYMVTGGQSLKKFHDLVCNGR

Parental  CKDIKLTYFIMIFASVHFVLSQLPNFNSISGISLAAAVMSLSYSTIAWGASL---HKGKEENVDYSLRAS
          C.DI.LT.FIMIF.SVHF.LSQ.PNFNSISG.S.AAAVMS..YS..A..AS....H......VDY.L.A.
Retrocopy CRDIRLTFFIMIFGSVHFLLSQMPNFNSISGVSAAAAVMSICYSMVAFFASVVHKHPVGAAVVDYGLKAT

Parental  TTAGQVFGFLGGLGDVAFSYSGHNVVLEIQATIPSTPGNPSKKPMWKGVVVAYIIIAACYFPVAFIGYWA
          .TAG.VFG....LG.VAF...GHNVVLEIQATIPSTP..PSKKPMW.GV.VAY.I.A.CYF.VAF.GY.A
Retrocopy STAGHVFGAFNALGAVAFAFAGHNVVLEIQATIPSTPEQPSKKPMWRGVMVAYAIVALCYFSVAFGGYYA

Parental  FGNSVDDNILITLNKPKWLIAMANMMVVVHLIGSYQIYAMPVFDMMETFLVKKLEFAPGITLRLITRTIY
          FGNSVD.NILITL.KP.WLIAMAN.MVVVH.IGSYQ..AMPVFDMMET.LVKKL.F.PG..LRL..R..Y
Retrocopy FGNSVDPNILITLDKPRWLIAMANLMVVVHVIGSYQVFAMPVFDMMETVLVKKLKFTPGLPLRLTARSAY

Parental  VAFTMFIGMSFPFFGGLIGFFGGLAFAPTTYFLPCIMWLIICKPRIFSLSWFTNWICIVLGVLLMIVAPI
          VA.TM.IGM.FPFF.GL.GFFGG.AFAPTTYFLPCI.WLI..KP...S..WF.NWI.IV.GVLLM...PI
Retrocopy VALTMLIGMTFPFFDGLLGFFGGFAFAPTTYFLPCIIWLILRKPARYSTTWFLNWIFIVIGVLLMLLSPI

Parental  GGLRQIIISAKTYKFYS
          GGLRQII..AKT.KFYS
Retrocopy GGLRQIILDAKTFKFYS

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_36 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_54046	1 retrocopy	retro_hvul_36 ,