RetrogeneDB ID: retro_hvul_24

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:181886871..181888224(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_7722
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_75040
• Aliases: None
• Description: None

Sequence

>retro_hvul_24
ATGGAGGAGCTCCGCAGCTCTATGCTTGTGGCTTTGATCCTCGCGGTCATGTGCTCCGTCGCAGTTGCCTACGATCCCCT
CGACCCCACAGGCAACATTACAATCAAATGGGATGTCCAGTCATGGACGCCCGACGGATACGTCGCCATGGTGACGATGA
ACAACTATCAGCAGTACCGCCAGATCATGTCGCCTGGATGGACGCTGGGGTGGTCGTGGGCCAAGAAGGAGGTGATCTGG
TCCATCGTGGGAGCGCAGGCGACGGAGCAGGGCGACTGCTCCAAGTTCAAGGGCGGCATCCCGCACTGTTGCAAGCACAC
GCCCTCCGTCGTCGACCTCCTCCCCGGCGTGCCCTACAACCAGCAGATCGCCAACTGCTGCCGTGGCGGCGTCGTCTCCG
CCTACGGCCAGGACCCCGCCGGCTCGCTCTCGGCGTTCCAGGTCTCGGTGGGGCTCGCCGGGACCACCAACAAGACCGTA
AAGCTTCCGAAGAACTTCACGCTCATGGGCCCCGGGCTCGGCTACACCTGTGGCCCCGCCACAATCGTCCCCTCCACCGT
CTACTGGAGCGCCGACCACCGGCGCAAGACTCAGGCGCTGATGACATGGACGGTGACCTGCACCTACTCGCAGCAGCTGG
CGTCCAGGTACCCGACCTGCTGCGTCTCCTTCTCCTCCTTCTACAACAGCACCATCGTGCCGTGCGCCAAGTGCGCGTGC
GGCTGCGGCGCCCACAAGAGCATGGGTGGGCGTGGCGGCAAGAGCCACAGCGACGGGTGCATCATGGGCGACTCCAAGCG
GGCGCTGACACCTGGGGTGAACACGCCCAAGAAGGACGGAGCGCAGCTGCTGCAGTGCACCAACCACATGTGCCCCATCC
GGGTGCACTGGCACGTCAAGCTCAACTACAAGGACTACTGGCGCGCCAAGATCGCCGTCACCAACTTCAACTACCGCATG
AACTACACGCAGTGGACGCTCGTCGCCCAGCATCCTAACCTCAACAACGTCACCGAGGTCTTCAGCTTCCAGTACAAACC
CCTCCTCCCCTACGGAAACATCAACGACACCGGCATGTTCTACGGCCTCAAGCTGTACAACGACCTGCTCATGGAGGCCG
GCCCCTTCGGCAACGTGCAGTCAGAGGTGCTCATGCGCAAGGACGACACAACCTTCACCTTCAGCCAGGGATGGGCGTTC
CCGCGCAAGATCTACTTCAACGGCGATGAGTGCAAGATGCCGCCGCCGGATTCCTACCCTTACCTGCCCAACGCCGCACC
GCTCGTGACACCGCGTTCCGTGATCACCGCTGCCTCGGCCTGCTTGCTCGTGCTCCTCCTCCTGGTGGCATGA

Alignment

ORF - retro_hvul_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.38 %
• Parental protein coverage: 99.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MELPNAALVLILAAAATLSVAVAYDPLDPNGNITIKWDVLSWTPDGYVATVTINNFQTYRQIMAPGWTVG
          ME.........L..A...SVAVAYDPLDP.GNITIKWDV.SWTPDGYVA.VT.NN.Q.YRQIM.PGWT.G
Retrocopy MEELRSSMLVALILAVMCSVAVAYDPLDPTGNITIKWDVQSWTPDGYVAMVTMNNYQQYRQIMSPGWTLG

Parental  WTWAKREVIWSMVGAQATEQGDCSKFKANLPHSCKRTPAVVDLLPGVPYNQQIANCCRGGVVSAYGQDPS
          W.WAK.EVIWS.VGAQATEQGDCSKFK...PH.CK.TP.VVDLLPGVPYNQQIANCCRGGVVSAYGQDP.
Retrocopy WSWAKKEVIWSIVGAQATEQGDCSKFKGGIPHCCKHTPSVVDLLPGVPYNQQIANCCRGGVVSAYGQDPA

Parental  GAVSSFQVSVGQAGTTNRTVKVPKNFTLLGPGPGYTCGPAKVVPSTVFLTADHRRKTQALMTWNVTCTYS
          G..S.FQVSVG.AGTTN.TVK.PKNFTL.GPG.GYTCGPA..VPSTV...ADHRRKTQALMTW.VTCTYS
Retrocopy GSLSAFQVSVGLAGTTNKTVKLPKNFTLMGPGLGYTCGPATIVPSTVYWSADHRRKTQALMTWTVTCTYS

Parental  QHLASKYPTCCVSFSSFYNDTIVPCAKCTCGC-EHKTCA--RSERDSKRLMSASGKSAVTARGHVNRQSA
          Q.LAS.YPTCCVSFSSFYN.TIVPCAKC.CGC..HK..........S........K.A.T..........
Retrocopy QQLASRYPTCCVSFSSFYNSTIVPCAKCACGCGAHKSMGGRGGKSHSDGCIMGDSKRALTPGVNTPKKDG

Parental  APLLQCTTHMCPVRVHWHVKLNYHDYWRAKVTVTNFNYRMNYTGWTLVAQHPNLDNITEVFSFDYKPVVS
          A.LLQCT.HMCP.RVHWHVKLNY.DYWRAK..VTNFNYRMNYT.WTLVAQHPNL.N.TEVFSF.YKP...
Retrocopy AQLLQCTNHMCPIRVHWHVKLNYKDYWRAKIAVTNFNYRMNYTQWTLVAQHPNLNNVTEVFSFQYKPLLP

Parental  YGSINDTALFYGMKFFNDQLMEAGPYGNVQSEVLMRKDASTFTFRQGWAFPRKIYFNGDECRMPPPDSYP
          YG.INDT..FYG.K..ND.LMEAGP.GNVQSEVLMRKD..TFTF.QGWAFPRKIYFNGDEC.MPPPDSYP
Retrocopy YGNINDTGMFYGLKLYNDLLMEAGPFGNVQSEVLMRKDDTTFTFSQGWAFPRKIYFNGDECKMPPPDSYP

Parental  YLPNSAP----ASLLSSASAVIVAFLVLL
          YLPN.AP.....S....ASA.....L.L.
Retrocopy YLPNAAPLVTPRSVITAASACLLVLLLLV

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_24 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_06160	1 retrocopy	retro_atau_16,
Hordeum vulgare	MLOC_75040	1 retrocopy	retro_hvul_24 ,