RetrogeneDB ID: retro_hvul_79

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:86014046..86014526(-)
• 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_79
GTGTTGTGTCCTCTGTACTACTACTACTACCAGCGGCACCCGGTGAACCTGCTGCTGCTGGCGCTCTTCACGGTGGCCAT
CAGCTTCGCGGTGGGGCTCACATGCGCCTTCACGAAGGGGGAGGTGATCCTGGAGTCGGCCATCCTGACGACTGTGGTGG
TGGTGAGCCTGACGGCGTACACCTTCTCGGCGGCGAGCCGTGGGCACGACTTCAACTTCCTGGGCCCGTTCCTGTTCGCG
GCGGTGATGATCCTCATGGTGTTCGCGCTCATCCACGCATTCTTCCCGCTGGGCCGCATCTCGCTCATGGTGTACGGCGG
GCTGGCGGCGCTCGTCTTCTGCGGCTACATCATCTACGACACCGACAACCTCATCAAGCGCTACTCCTACGACGAGTACA
TCTGGGCCGCCGTCGCGCTCTACCTCGACGTCATCAACCTCTTCCTCTCCCTGCTCACCCTCTTTAGGGCATCCGATTCC

Alignment

ORF - retro_hvul_79 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.12 %
• Parental protein coverage: 71.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLCPLRYYH-QKHPVNLILLGIFTVSISFAVGMTCAFTSGKIILEAAILTAVVVISLTAYTFWAAKRGHD
          VLCPL.YY..Q.HPVNL.LL..FTV.ISFAVG.TCAFT.G..ILE.AILT.VVV.SLTAYTF.AA.RGHD
Retrocopy VLCPLYYYYYQRHPVNLLLLALFTVAISFAVGLTCAFTKGEVILESAILTTVVVVSLTAYTFSAASRGHD

Parental  FNFLGPFLFGALMVLMMFSLIQIFFPLGKISVMIYGAVASIIFCGYIIFDTDNIIKRYTYDEYIWAAVSL
          FNFLGPFLF.A.M.LM.F.LI..FFPLG.IS.M.YG..A...FCGYII.DTDN.IKRY.YDEYIWAAV.L
Retrocopy FNFLGPFLFAAVMILMVFALIHAFFPLGRISLMVYGGLAALVFCGYIIYDTDNLIKRYSYDEYIWAAVAL

Parental  YLDIINLFLNLMQILRAADS
          YLD.INLFL.L....RA.DS
Retrocopy YLDVINLFLSLLTLFRASDS

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_79 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.

---

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 ,