RetrogeneDB ID: retro_hvul_5

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:305262844..305263783(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_22881
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_58678
• Aliases: None
• Description: None

Sequence

>retro_hvul_5
ATGCTGGCGGCGCTGCGGGATTGGAAGATCGCGTCGGCGTACGAGACGTTTCCGTGGGAGAAGAAGATGAAGTCGCTGCT
GCCGGTGCCGGAGTCGAGCCGGTTCCTGTCGCTGCTGCTGCTCCCCAAGGCCACGGACGGCACCCACACCCGCTACAACT
CGCTGGACGACACCCTCGCCCGCGCCGACGCCTGGCTCGCCTCGTCCCGCGCCTCCGGTGTCCCCGTCGAGCTCGCCAGC
GTCCAGACGGAGGCGCTGCTCACCAAGATCTCCGGCGAGACGGCGGTGTCCACGGTGAACATGGGGTCCCTGTCCGACCT
GGCCAACATGTCCAACGTGAGCCTGTACGGGTTCGAGGACTACCACGGCGTGGACATCGGCGTGGTGCGCGCGGTGCGGC
TGTGGTACGCGCCGTCGGGCCCCGGCGGCGAGATGGCGGTGGAGATCGCGCTGCGGCAGGGGGACACCAGGCTCGGCTTC
GCCATCAGCCGGACCGAGGAAGGGTTCATCTACGTGTCGTCGGTGGCGGACGAGAGCACGCCCGGCGTGGCGTCCACGCG
GTCGGGGCTGCTCGAGCTGCACCGGGCGGCGAGGCGGGCGGGCAGGCTGCTGGTGGTTTCGAGGGTGGGAGGGGAGAAGG
TGCTGCCGTGGCTGGTCTCCACCGCCGGCGACGTCAGGTGCTACGACACCGTGTCGCTGAGCCAGAAGCTCTCGCTGCAC
CGCCACGCGCTCCGCCCCATCACGCTGCACTTCCTCACGTGGGACGAGGGCGCCCTCGCCCTGCCTCCGCCGCCGGCGCC
GGCGCCGCTGCTCATGCTGTCGTCCGAAGGCGACGAGGAGGAGATCGATGGCGACGGGCCGGAGATCGCGGCCGGCAAGG
GCGGCAAGGGCTCGTCCTTTAGGTTCCAGAACATCGGACTACCGGATAGCTGGCTGTGA

Alignment

ORF - retro_hvul_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.7 %
• Parental protein coverage: 69.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVCALSKAQLQDGYVSYPWEKKMKEVLPVPSSSSFLSLLVLPTALDRANSRYNSVDDTLARANAWFLSSQ
          ...AL........Y...PWEKKMK..LPVP.SS.FLSLL.LP.A.D....RYNS.DDTLARA.AW..SS.
Retrocopy MLAALRDWKIASAYETFPWEKKMKSLLPVPESSRFLSLLLLPKATDGTHTRYNSLDDTLARADAWLASSR

Parental  AAGVPIAFLNVQTEALLTKISGDMASATVNSGSLADLPNLANASLYGFEDYHGVDIGVVKAVRLWF--TA
          A.GVP.....VQTEALLTKISG..A..TVN.GSL.DL.N..N.SLYGFEDYHGVDIGVV.AVRLW.....
Retrocopy ASGVPVELASVQTEALLTKISGETAVSTVNMGSLSDLANMSNVSLYGFEDYHGVDIGVVRAVRLWYAPSG

Parental  AAGEMPVEIILDEGDTKLGFAISRTEEGFLYISSVMEDDGDRPAPSTRSGLRDLYREAKRASKLLVISRV
          ..GEM.VEI.L..GDT.LGFAISRTEEGF.Y.SSV..D.......STRSGL..L.R.A.RA..LLV.SRV
Retrocopy PGGEMAVEIALRQGDTRLGFAISRTEEGFIYVSSV-ADESTPGVASTRSGLLELHRAARRAGRLLVVSRV

Parental  SCRKVLPWMVSTSGAIRCFDTVSLSQKLSLHRHALRPILLHVLMWDFGTDAPNRPAQGAP
          ...KVLPW.VST.G..RC.DTVSLSQKLSLHRHALRPI.LH.L.WD.G..A...P...AP
Retrocopy GGEKVLPWLVSTAGDVRCYDTVSLSQKLSLHRHALRPITLHFLTWDEGALALPPPPAPAP

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_5 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_58678	1 retrocopy	retro_hvul_5 ,