RetrogeneDB ID: retro_hvul_82

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:497455763..497456483(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_27126
• Aliases: None
• Description: None

Sequence

>retro_hvul_82
TTCGTGGGGGCGTCAATGGGGACGTCCCAGCTGAAGATACCAGCGGCGAAGAAGGGCGGCAGTAGCCACGGGCCAGGCCA
GCGCTGCGTGGTGGTGGTGGAGTACCAGCACGGCGGCACCCTGAAGACTCTGCTGTTCCAGCACCGGGACAAGAAGCTGC
CATACAAGAAGGTGGTCCAGCTGGCGCTGGACATGGCGAGAGGGCTGAACTACCTGCACTCGCAGAAGATCGTGCACCGG
GACGTGAAGGCGGAGAACATGCTGCTGGACAGGAAGAAGTCGGTGAAGATTGCTGATTTCGGGGTGGCGCGGGTGGAGGC
GCAGGACGACGACAACATGACGGGGCAGACGGGCACGCTGGGGTATATGGCCCCCGAGGTGCTGGAGGGGCGGCCGTACG
ACCACAAGTGTGACGTGTACAGCTTCGGCGTCCTGCTGTGGGAGACGTACTGCTGCGCCTTGGCATACCCGAACTACAGC
ATCGCCGACATCTCGTACCACGTGGTGAAGCTGGGCATCCGGCCCGACATCCCGCGGTGCTGCCCCAAGCCGCTGTCGGA
GATCATGACGCGGTGCTGGGACGGCAACCCGGACCACCGGCCGGAGATGGCGGAGGTGGTGGCGATGCTGGAGAGGATCG
ACACCACCAAGGGCAAGAGCATGACCCCCGCCGTCCCCGAGCACAGCTCGCAGGGCTGCAGCTGCTTCGGCTTTGCCAAG

Alignment

ORF - retro_hvul_82 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.08 %
• Parental protein coverage: 63.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FVGASMGTTDLKIPVNDNGARANLPARACCVVVEYLAGGTLKQYLIKNRRRKLAYKVVVQLALDLSRGLS
          FVGASMGT..LKIP....G.....P...C.VVVEY..GGTLK..L...R..KL.YK.VVQLALD..RGL.
Retrocopy FVGASMGTSQLKIPAAKKGGSSHGPGQRCVVVVEYQHGGTLKTLLFQHRDKKLPYKKVVQLALDMARGLN

Parental  YLHSRKIVHRDVKTENMLLDTQRNLKIADFGVARVEAQNPKDMTGATGTLGYMAPEVLDGKPYNRKCDVY
          YLHS.KIVHRDVK.ENMLLD.....KIADFGVARVEAQ....MTG.TGTLGYMAPEVL.G.PY..KCDVY
Retrocopy YLHSQKIVHRDVKAENMLLDRKKSVKIADFGVARVEAQDDDNMTGQTGTLGYMAPEVLEGRPYDHKCDVY

Parental  SFGICLWEIYCCDMPYPDLSFADVSSAVVHQNLRPDIPRCCPSAFANIMRKCWDGNPDKRPDMDEVVQLM
          SFG..LWE.YCC...YP..S.AD.S..VV....RPDIPRCCP.....IM..CWDGNPD.RP.M.EVV...
Retrocopy SFGVLLWETYCCALAYPNYSIADISYHVVKLGIRPDIPRCCPKPLSEIMTRCWDGNPDHRPEMAEVVAML

Parental  EALDTSKGGGM---IPDGQSSGCLCFTRAR
          E..DT.KG..M....P...S.GC.CF..A.
Retrocopy ERIDTTKGKSMTPAVPEHSSQGCSCFGFAK

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_82 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_27126	1 retrocopy	retro_hvul_82 ,
Oryza sativa japonica	OS03G0638800	2 retrocopies	retro_osat_62, retro_osat_81,