RetrogeneDB ID: retro_hvul_8

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 2:411471582..411472890(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_62122
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_50327
• Aliases: None
• Description: None

Sequence

>retro_hvul_8
ATGGCCGTGCCCACCAACGACTCCGCCGTGCGCGCGCGCCTCCGCCGTCTCGGCGAGCCCATCACGCTCTTCGGCGAGGG
CGCGATGGAGCGCCGCGACCGGCTACGCGCACTCATGGCCCGCCTCGAGGCCGAGGGCCAGTTCGACCGCCTCCTCCGCG
CGCAGGAGGACGAACAGGGAGCCCCGGGCGACGACGAGGAGGACACGGAGGAGCAGATCAAGTACCCGTTCTTCACCGAG
GGGACCAACCAACTGCTCCAGGCGCGCGTTGACATCGCCATGTACTCGCTGCCCCGCGCCAAGGCCAGGGTCGAGAGGGC
CAAGCGACGACTCGCCGACCCCGACGAGGACCCCGAGGCAGAGGCCGGACTTGTTGTGAAGCAGGCGGCGGACTTCGTGC
TTGAGTGCAGCGAGATTGGAGATGACCGCCCGCTCACCGGCTGCTCCTTCTCCCGCGACGCCTCGATGCTCGCCACAAGT
TCCTGGAGCGGAATCGTCAAAGTATGGAGCATGCCGCAGATAACCAAAATTGCAACCCTGAAAGGTCATACAGAACGCGC
AACTGATGTTGCCTTCTCTCCAGTCGATAACTGCTTAGCGACAGCCTCAGCTGATAGAACTGCCAAATTGTGGAACAGCC
ATGGGTCACTTCTAATGTCCTTTGATGGTCACCTGGATCGTCTTGCTCGCCTTGCTTTTCATCCATCTGGAAAGTACCTT
GGCACAGCTAGCTTTGACAAGACCTGGAGATTATGGGACATCAATACTGGAACTGAACTTCTACTCCAGGAGGGGCATAG
CAGAAGTGTATATGATCTTAGCTTTCACCCTGACGGTTCTTTAGCTGCATCTTGTGGGTTTGATGCGACTGCTCGAGTTT
GGGATCTCAGATCAGGAAGATTGTACTGTACCCTCATTGGACATGTGAAGCCTGTCCTAGGAGTCAGCTTCTCCCCTAAT
GGTCATCTGGTTGCAACCGCAAGTGAAGACAATTTCTGTCGAATATGGGATTTGAGGACCAGACAAATGATTTATTCTAT
ACCAGCACATAAGAGTCTTATCTCACATGTGAAATTTGAACCCCAGGAGGGTTATTATTTAGTGACATCTTCCTATGACA
CTAAAGCAGCGCTGTGGTCAACTCGGGATTACAGACCAATTAAAAGCTTGTCAGGCCATGAGTCAAATGTTTCTAGTCTG
GATATCAGTGGAGATGGACAACAGATTGTGACTGTTTCACACGATAGAACGATAAAGATTTGGTCATGCAGAGGCAGCGC
GCGGGATGATGAGATGGAGTTGGATTAA

Alignment

ORF - retro_hvul_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.92 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVPTNDSAVRTRLRRLSEPITLFGEREMERRDRLRALMVRLEADAQFDRLLRAQEDEQGAPDDDDT---
          MAVPTNDSAVR.RLRRL.EPITLFGE..MERRDRLRALM.RLEA..QFDRLLRAQEDEQGAP.DD.....
Retrocopy MAVPTNDSAVRARLRRLGEPITLFGEGAMERRDRLRALMARLEAEGQFDRLLRAQEDEQGAPGDDEEDTE

Parental  EQIQYPFFTEGTNQLLQARLDIAMYSLPRAKARVDRAKRRLADPDEDPEAEAGLVVKQAGDFVLECSEVG
          EQI.YPFFTEGTNQLLQAR.DIAMYSLPRAKARV.RAKRRLADPDEDPEAEAGLVVKQA.DFVLECSE.G
Retrocopy EQIKYPFFTEGTNQLLQARVDIAMYSLPRAKARVERAKRRLADPDEDPEAEAGLVVKQAADFVLECSEIG

Parental  DDRPLTGCSFSGDASMLATSSWSGIIKVWSMPQITKIATLKGHRERATDVAFSPVDNCLATASADKTAKL
          DDRPLTGCSFS.DASMLATSSWSGI.KVWSMPQITKIATLKGH.ERATDVAFSPVDNCLATASAD.TAKL
Retrocopy DDRPLTGCSFSRDASMLATSSWSGIVKVWSMPQITKIATLKGHTERATDVAFSPVDNCLATASADRTAKL

Parental  WNSDGSLLMSFDGHLDRLARVAFHPSGKYLGTASFDKTWRLWDINTGTELLLQEGHSRSVYGVSFHPDGS
          WNS.GSLLMSFDGHLDRLAR.AFHPSGKYLGTASFDKTWRLWDINTGTELLLQEGHSRSVY..SFHPDGS
Retrocopy WNSHGSLLMSFDGHLDRLARLAFHPSGKYLGTASFDKTWRLWDINTGTELLLQEGHSRSVYDLSFHPDGS

Parental  LAASCGLDANARVWDLRSGRLYCTLIGHVKPVLGVSFSPNGHLVATASEDNFCRIWDLRTRQMLYSIPAH
          LAASCG.DA.ARVWDLRSGRLYCTLIGHVKPVLGVSFSPNGHLVATASEDNFCRIWDLRTRQM.YSIPAH
Retrocopy LAASCGFDATARVWDLRSGRLYCTLIGHVKPVLGVSFSPNGHLVATASEDNFCRIWDLRTRQMIYSIPAH

Parental  KSLISYVKFEPQEGYYLATSSYDTKAAVCFICDFGSI
          KSLIS.VKFEPQEGYYL.TSSYDTKAA.....D...I
Retrocopy KSLISHVKFEPQEGYYLVTSSYDTKAALWSTRDYRPI

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_8 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_19450	1 retrocopy	retro_atau_1,
Hordeum vulgare	MLOC_50327	1 retrocopy	retro_hvul_8 ,
Triticum aestivum	Traes_4AL_060131441	1 retrocopy	retro_taes_21,