RetrogeneDB ID: retro_hvul_34

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 2:17582363..17583026(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_48245
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_80447
• Aliases: None
• Description: None

Sequence

>retro_hvul_34
ATGCTCGTCGCGCACAAGCGCTTCCTCGTGCGCATCCCGGACGCCCTCCCGCTGGACGCCGCCGCGCCGCTGCTGTGCGC
CGGGATCACCGTGTACAGCCCCATGAAGCAGCACGGGATGCTGCACGCTGGCAGGAGGCTCGGCGTGGTCGGGCTGGGCG
GGCTCGGCCACGTCGCCGTCAAGTTCGGCAAGGCCTTCGGGCTCAAGGTCACCGTCATCAGCACGTCGCCGGCCAAGGAG
CGCGAGGCCAGGGAGAGCCTCAAGGCCGACGACTTCGTCCTCAGCACCGACGACAAGCAGATGCAGGCCATGGCGAGGAG
CCTGGACTACGTGATCGACACGGTGTCGACGCAGCACTCGCTGGGGCCCATCCTGGAGCTGCTCAAGGTGAACGGCAAGC
TGGTGCTGGTGGCGGCGCCGGACAAGCCCGTGGAGCTGCCGTCCTTCCCGCTCATCTTCGGGAAGAGGACGGTGAGCGGG
AGCATGACTGGGGGCATGAAGGAGACGCAGGAGATGATGGACCTGTGCGGGGAGCACGGCATCACCGCCGACATCGAGCT
CGTCTCCACCGACGGGATCAACGACGCGCTGGCCAGGCTCGCGCGCAACGACGTGCGCTACCGCTTCGTCGTCGACGTCG
CCGGGAATGGCTCCAGGCTCTAG

Alignment

ORF - retro_hvul_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.88 %
• Parental protein coverage: 65.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVVVHERFVVRFPDAMPLDKGAPLLCAGITVYSPMKYHGLNVPGLHLGVLGLGGLGHVAVKFGKAFGMKV
          M.V.H.RF.VR.PDA.PLD..APLLCAGITVYSPMK.HG....G..LGV.GLGGLGHVAVKFGKAFG.KV
Retrocopy MLVAHKRFLVRIPDALPLDAAAPLLCAGITVYSPMKQHGMLHAGRRLGVVGLGGLGHVAVKFGKAFGLKV

Parental  TVISSSPGKKQEALERLGADAFVVSKDADEMKAAVSTMDGIINTVSANIPMAPLLGLLKPNGKMIMVGLP
          TVIS.SP.K..EA.E.L.AD.FV.S.D...M.A.....D..I.TVS......P.L.LLK.NGK...V..P
Retrocopy TVISTSPAKEREARESLKADDFVLSTDDKQMQAMARSLDYVIDTVSTQHSLGPILELLKVNGKLVLVAAP

Parental  EQPIEVPPFALVARNKTLAGSCIGGMRDTQEMLDLAAKHGVTADIEVISAEYVNTAMERLAKADVRYRFV
          ..P.E.P.F.L.....T..GS..GGM..TQEM.DL...HG.TADIE..S....N.A..RLA..DVRYRFV
Retrocopy DKPVELPSFPLIFGKRTVSGSMTGGMKETQEMMDLCGEHGITADIELVSTDGINDALARLARNDVRYRFV

Parental  IDIA
          .D.A
Retrocopy VDVA

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_34 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_80447	2 retrocopies	retro_hvul_34 , retro_hvul_42,