RetrogeneDB ID: retro_hvul_40

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 1:270045143..270046625(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_74069
• Aliases: None
• Description: None

Sequence

>retro_hvul_40
GACGACACCGTCCAAGGGATGACCGGAAACCTGTTCGACGCCTTCCTGAGACCCTACTTCCTTGAGGCCTACCGTCCGCT
CAGAAAGGGAGACCTGTTCCTGGTGAGAGGCGGCATGACGAGCGTGGAGTTCAAGGTCGTGGAGACCGACCCCGCGGAGT
ACTGCATCGTCGCTCCTGACACGGAGGTTTTCTGCGACGGCGAGCCTGTCAAGAGGGAGGACGAGGAGAGGCTCGACGAC
GTCGGCTACGACGATGTCGGCGGAGTCAGGAAGCAGATGGCCCAGATCAGAGAGCTGGTTGAGCTCCCGCTGCGCCACCC
CCAGCTGTTCAAGTCCATTGGTGTCAAGCCTCCGAAGGGCATCTTGCTGTATGGGCCACCTGGGACCGGCAAAACCCTCA
TTGCCAGAGCTGTGGCCAACGAGACAGGCGCCTTCTTCTTCCTGATCAATGGCCCGGAGATTATGTCGAAGCTCGCCGGA
GAAAGCGAGAGCAACCTCAGGAAGGCGTTTGAAGAGGCCGAGAAGAACGCGCCGGCCATCATCTTCATCGACGAGATTGA
CTCCATAGCCCCAAAGAGAGAAAAGACCAACGGAGAGGTGGAAAGGCGTATCGTTTCGCAGCTGCTCACTCTCATGGATG
GGCTTAAGTCCCGTGCACACGTTATTGTCATGGGTGCTACCAACCGCCCGAACAGCATCGACCCTGCTCTCAGAAGGTTT
GGAAGGTTTGATAGAGAGATCGACATTGGAGTCCCCGATGAGGTCGGGCGGCTCGAGGTTCTCCGGATTCACACTAAGAA
CATGAAGCTGGCTGAAGATGTTGAGCTGGAGCATGTTTCAAGAGACACCCATGGGTACGTCGGCGCCGATCTCGCTGCCC
TTTGTACCGAGGCTGCTCTCCAGTGCATTCGCGAGAAGATGGATATCATAGACCTCGAGGATGACACCATTGATGCGGAG
ATACTGAATTCCATGGCCGTCACAAATGACCATTTCAAGATTGCACTGGGGACAAGCAACCCATCTGCTCTTCGTGAAAC
TATGGTCGAAGTTCCGAATGTCTCTTGGGAAGATATTGGTGGCCTGGAGAGTGTAAAAAGGGAGCTGCAGGAGACCGTCC
AGTATCCAGTGGAGCATCCAGAGAAATTCGAGAAGTTTGGCATGGCTCCCTCCAAAGGTGTTCTGTTCTACGGCCCTCCG
GGCTGCGGCAAGACCTTGTTGGCCAAGGCGATTGCCAATGAGTGCCAGGCAAACTTCATCAGCATCAAAGGACCGGAGCT
GCTTACCATGTGGTTTGGCGAGAGCGAGGCCAATGTGCGTGAGATCTTCGACAAGGCTAGGGGGTCGGCACCATGCGTCC
TCTTCTTTGACGAGCTCGACTCGATTGCCACCAAGCGAGGAAGCAGTGTTGGCGATGCCGGAGGTGCCGCCGATAGGGTG
CTGAATCAGCTTCTTACCGAGATGGACGGCATGAATGCCAAG

Alignment

ORF - retro_hvul_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.56 %
• Parental protein coverage: 78.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDTVEGITGNLFDAFLKPYFLEAYRPLRKGDLFLVRGGMRSVEFKVIETDPAEYCIVAPDTEIFCDGEPV
          DDTV.G.TGNLFDAFL.PYFLEAYRPLRKGDLFLVRGGM.SVEFKV.ETDPAEYCIVAPDTE.FCDGEPV
Retrocopy DDTVQGMTGNLFDAFLRPYFLEAYRPLRKGDLFLVRGGMTSVEFKVVETDPAEYCIVAPDTEVFCDGEPV

Parental  KREDEERLDDVGYDDVGGVRKQMAQIRELVELPLRHPQLFKSIGVKPPKGILLFGPPGSGKTLIARAVAN
          KREDEERLDDVGYDDVGGVRKQMAQIRELVELPLRHPQLFKSIGVKPPKGILL.GPPG.GKTLIARAVAN
Retrocopy KREDEERLDDVGYDDVGGVRKQMAQIRELVELPLRHPQLFKSIGVKPPKGILLYGPPGTGKTLIARAVAN

Parental  ETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPSIIFIDEIDSIAPKREKTNGEVERRIVSQLLT
          ETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAP.IIFIDEIDSIAPKREKTNGEVERRIVSQLLT
Retrocopy ETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKREKTNGEVERRIVSQLLT

Parental  LMDGLKSRAHVIVMGATNRPNSIDPALRRFGRFDREIDIGVPDEVGRLEVLRIHTKNMKLAEDVELEHIS
          LMDGLKSRAHVIVMGATNRPNSIDPALRRFGRFDREIDIGVPDEVGRLEVLRIHTKNMKLAEDVELEH.S
Retrocopy LMDGLKSRAHVIVMGATNRPNSIDPALRRFGRFDREIDIGVPDEVGRLEVLRIHTKNMKLAEDVELEHVS

Parental  RDTHGYVGADLAALCTEAALQCIREKMDIIDLEDETIDAEILNSMAVTNDHFKTALTTSNPSALRETVVE
          RDTHGYVGADLAALCTEAALQCIREKMDIIDLED.TIDAEILNSMAVTNDHFK.AL.TSNPSALRET.VE
Retrocopy RDTHGYVGADLAALCTEAALQCIREKMDIIDLEDDTIDAEILNSMAVTNDHFKIALGTSNPSALRETMVE

Parental  VPNVSWEDIGGLENVKRELQETVQYPVEHPEKFEKFGMSPSKGVLFYGPPGCGKTLLAKAIANECQANFI
          VPNVSWEDIGGLE.VKRELQETVQYPVEHPEKFEKFGM.PSKGVLFYGPPGCGKTLLAKAIANECQANFI
Retrocopy VPNVSWEDIGGLESVKRELQETVQYPVEHPEKFEKFGMAPSKGVLFYGPPGCGKTLLAKAIANECQANFI

Parental  SIKGPELLTMWFGESEANVREIFDKARGSAPCVLFFDELDSIATQRGSSVGDAGGAADRVLNQLLTEMDG
          SIKGPELLTMWFGESEANVREIFDKARGSAPCVLFFDELDSIAT.RGSSVGDAGGAADRVLNQLLTEMDG
Retrocopy SIKGPELLTMWFGESEANVREIFDKARGSAPCVLFFDELDSIATKRGSSVGDAGGAADRVLNQLLTEMDG

Parental  MNAK
          MNAK
Retrocopy MNAK

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_40 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G74922	1 retrocopy	retro_bdis_9,
Leersia perrieri	LPERR03G03650	1 retrocopy	retro_lper_1,
Hordeum vulgare	MLOC_74069	2 retrocopies	retro_hvul_38, retro_hvul_40 ,
Hordeum vulgare	MLOC_76416	1 retrocopy	retro_hvul_59,
Oryza glaberrima	ORGLA06G0255900	1 retrocopy	retro_ogla_73,
Populus trichocarpa	POPTR_0006s12740	1 retrocopy	retro_ptri_3,
Sorghum bicolor	Sb01g020910	1 retrocopy	retro_sbic_10,