RetrogeneDB ID: retro_hvul_19

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 3:459904568..459906311(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_18180
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_67221
• Aliases: None
• Description: None

Sequence

>retro_hvul_19
ATGGCCAATGGACACCGTGCTCCACTACTCACAGCCTGCGTGTTCCTCATCATCTGCGCCGCCGCCACGCTCGTCGTCGT
CTACACCGCCTTCCCGGTCTCCCTGAACCCATGCACCTACTCTCTGCCGAGGGCGCTCATCACCGTCTCCGGCCTCCACC
CGTACGTCGTCTCATGCCAAGGCGACGCCGACACCGCCCCACTCTCCGACGGCAGCAAGAAGACCGGCGGTCCTGTCGAG
ACCAGCCTACGCACGTGCGTGAAGCCAACACTCCCGCCGCACCCGCTCCCGCCCTTCTACTGCTGCCCGCCGGCGCCCGC
GTCGGAGCCGATCAACTTCACGCTCCCGGACCCGGCCGAGCCGGTCAGGGTCCGGCGGCCGACCCACGCCGCGGGGGCGG
CGGAGCACATGGCCAAGTACGAGCGCGCGATAGCGCTGATGCGCGCGCTGCCGGACGACGACCCGCGCAGCTTCTACCAG
CTGGCCAACGTCCACTGCGCCTACTGCACCGGCTCCTACCGCCAGACGGGGCACCCGGAGCTCCACATGCAGATCCACTT
CTCGTGGCTCTTCTTCCCCTTCCACCGCGCCTACCTCTACTTCTTCGAGCGCATCGCGGCGAGGCTGCTCGGCGATCCCG
GCTTCGCGCTGCCCTTCTGGGGCTGGGACGTGCCGGAGGGGATGCGGATGCCGGCCGAGTTCGCCAACTCCTCGTCGCCG
CTCTACGACCCCGCGCGGAACCCGGCGCACGCGCCGCCCGCGGTCGTCGACCTGGACTTCGCGCGCGTCGAGGGCAACCT
CACCGACGAGCAGCGGGTCCAGCAGAACCTCAGGATCATGTACAGGCAGATGGTCGGCAATGCGGCCCTGCCGTCCCTCT
TCCACGGCCAGCCCTTCCGTGCCGGCCAGTCCGACATGCCGGGCGCTGGGACGGTGGAGCTCACCCCGCACAACGCCATG
CACACCTGGACCGGCGATCTCACCCTCCGCAACGTGGAGGACATGGGCACCTACTACTCCGCCGGCCGAGACCCGCTCTT
CTACCCGCACCACGGCAACATCGACCGCCTGTGGGAGGCGTGGCGCGACGTCGGCGCCGCCCGCGGCTACCGCGGTCACG
TCGACTTCACGGACCCCGACTGGCTCGACTCCTCCTTCCTCTTCTACGACGAGGAGGCCCGCCTGGTGCGGATCACCGTC
CGCGACGTGCTCGACGTCGACAAGCTCCGGTACAGGTTTGACGACGTTGGCATGCCGTGGGCCGACGCGCGTCCGTCTCC
TACTCCAAACGTGAACGGAAATAAACCTAGCTCCTCGTCGTCGTCGTTGAAGTCCGTCAGCTTCCCGCTGTCCCTTCACA
CGGCTGTGACCGTGGAGGTAAGACGGCCGCGGGTGCTTCGAGGCCGGCCGGAGAAGGAGGTGCACGAGGAGGTGCTGGTG
GTCGAGGGCATCGAGACCGACGGCACGGAAATGGTCAAGTTCGACGCCTACGTGAACGCCATGGAGTACGAGAAGGTCGG
GCCGAGCGGGCGGGAGCTGGCCGGGAGCTACCTGTGCTTGAGCCATCCTAGTACGGATGGCACAGGGAAGGGGATGACGG
TGGAGACGAGCATGAGGATGGCGTTGAACGAGCTCTTGGAAGATCTGGGCGCCGACGGAGACGAGAGTGTGACGGTGACA
TTGGTACCTAGACACGGGAAGGTTAAGATCGGAGGCCTGAAAATTGTGTACATGATGGAGTGA

Alignment

ORF - retro_hvul_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.63 %
• Parental protein coverage: 52.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGAAAAGLGAQRDALAAPIQAPDFLNCNPPDLPNTP-PDASCCPPYRDGTIITDFRPPPASSPLRVRPAA
          G.A..A.L.........P........C..P.LP..P.P...CCPP......I....P.PA..P.RVR...
Retrocopy GDADTAPLSDGSKKTGGPVET-SLRTCVKPTLPPHPLPPFYCCPPAPASEPINFTLPDPAE-PVRVRRPT

Parental  HLVDA-ESLAKYERAVALMKQLPADDPRSFEQQWRVHCAYCGAVFDQVGFPDLEIQIHFCWLFFPWHRLY
          H...A.E..AKYERA.ALM..LP.DDPRSF.Q...VHCAYC.....Q.G.P.L..QIHF.WLFFP.HR.Y
Retrocopy HAAGAAEHMAKYERAIALMRALPDDDPRSFYQLANVHCAYCTGSYRQTGHPELHMQIHFSWLFFPFHRAY

Parental  LYFHERILGKLIGDDTFALPFWNWDAPDGMSLPAIYANGSSPLYNERRDPAHQPPFPLDLDYSDTDANIS
          LYF.ERI...L.GD..FALPFW.WD.P.GM..PA..AN.SSPLY...R.PAH.PP...DLD......N..
Retrocopy LYFFERIAARLLGDPGFALPFWGWDVPEGMRMPAEFANSSSPLYDPARNPAHAPPAVVDLDFARVEGNLT

Parental  RDQLIDQNLKIMYRQMVSDAKKRELFLGQPYRAGDQPDTGAGSVENVPHGPVHRWTGDPAQPNREDMGNF
          ..Q...QNL.IMYRQMV..A....LF.GQP.RAG.....GAG.VE..PH...H.WTGD....N.EDMG..
Retrocopy DEQRVQQNLRIMYRQMVGNAALPSLFHGQPFRAGQSDMPGAGTVELTPHNAMHTWTGDLTLRNVEDMGTY

Parental  YSAARDPIFFAHHGNIDRLWHVWR
          YSA.RDP.F..HHGNIDRLW..WR
Retrocopy YSAGRDPLFYPHHGNIDRLWEAWR

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_19 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_67221	1 retrocopy	retro_hvul_19 ,