RetrogeneDB ID: retro_hvul_74

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:517619235..517619709(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_34672
• Aliases: None
• Description: None

Sequence

>retro_hvul_74
GTGATGCTGCCGATGGTCTACTTCCGGAAGAAGCACCCGGTGAACCTGGTGTTCCTGGGCATCTTCACCGTGTGCATCAG
CCTGTCGATAGGGCTGGGGTGCCTCACCAAGCGCGGGCCCATCATCTTCGAGGCGGCCGGCATGACGCTCGTCGTCGTGG
TCTCGCTCACCGCCTACACCTTCTGGGCGGCCAAGCGCGGACACGACTTCGAGTTCCTCGGCCCCTTCCTCTTCGCCGCG
TGCGTCATCCTCCTCCTCTACGCCATCGTCATTGTGCTCTTCCCCATGGGCAAGACGACGGTGCTCGTCTATGGCTGCAT
CGCCGCGCTCATCTTCTCCGCCTTCATCATCTACGACACCGACAACCTCATCAAGCGCTACACCTACGACGAGTATGTCG
CCGCCTCCATTACCCTCTACCTCGACATCATCAACCTCTTCAGGGCCATCCTAATCGCCCTCGAGGCCGCCGAC

Alignment

ORF - retro_hvul_74 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.86 %
• Parental protein coverage: 71.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLCPLRYYHQKHPVNLILLGIFTVSISFAVGMTCAFTSGKIILEAAILTAVVVISLTAYTFWAAKRGHDF
          V..P..Y...KHPVNL..LGIFTV.IS...G..C....G.II.EAA..T.VVV.SLTAYTFWAAKRGHDF
Retrocopy VMLPMVYFRKKHPVNLVFLGIFTVCISLSIGLGCLTKRGPIIFEAAGMTLVVVVSLTAYTFWAAKRGHDF

Parental  NFLGPFLFGALMVLMMFSLIQIFFPLGKISVMIYGAVASIIFCGYIIFDTDNIIKRYTYDEYIWAAVSLY
          .FLGPFLF.A...L.........FP.GK..V..YG..A..IF...II.DTDN.IKRYTYDEY..A...LY
Retrocopy EFLGPFLFAACVILLLYAIVIVLFPMGKTTVLVYGCIAALIFSAFIIYDTDNLIKRYTYDEYVAASITLY

Parental  LDIINLFLNLMQILRAAD
          LDIINLF......L.AAD
Retrocopy LDIINLFRAILIALEAAD

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_74 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_34672	3 retrocopies	retro_hvul_74 , retro_hvul_78, retro_hvul_79,