RetrogeneDB ID: retro_hvul_38

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 1:129035156..129037016(+)
• 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_38
CCCATGGCGATCCACGGCGAGCCCTCTTCCTCCGATCCGAGCGGGAAGAAGGACTACTCCACGGCGATTCTTGAGAGGAA
GAAGTCACCGAACCGGCTGGTGGTCGACGAGGCCACCCGCGACGATAACTCCGCCGTCGCTCTACACCCGGACACCATAG
ACAGGCTGCAGCTCTTCACCGGCGACACGCTCCTGCTCAAGGGCAAGAAGCGGAAAGACACGGTCTGCATTGCGCTACCC
GACGACACGTGCGAGCATACCAAGATCCGGATGAACAAGGTCGTCAGGAAGAACCTGAGGGTGCGGCTCGGCGACGTCGT
CTCTATTCATCAGTGCCCAGACGTCAAATACGGGAAGCGCGTGCACGTACTTCCCATCGACGACACGGTGGAAGGGATCG
ACGGAAACCTGTTCGAAGCCTTCCTGAGACCATACTTCCTCGAAGCCTATCGACCCGTCAGAAAAGGAGACCTTTTCCTT
GTGAGAGGCGGGATGACAAGTGTGGAGTTCAAAGTCATAGAGACTGACCCTGCAGAGTATTGCATCGTCGCGCCTGATAC
AGAGATATTCTGCGACGGCGAACCGGTCAGGAGGGAGGATGAGGAGAAGCTGGACGATGTCGGCTACGACGATGTCGGTG
GGGTCAGGAAACAGATGGCCCAGATCAGAGAGCTGGTTGAGCTCCCACTGCGCCATCCCCAGCTGTTCAAGTCCATTGGT
GTGAAGCCTCCCAAGGGCATCTTGCTGTATGGGCCACCTGGGACTGGCAAGACCCTCATTGCTAGAGCTGTGGCCAATGA
AACAGGTGCCTTCTTTTTCCTGATTAATGGCCCAGAGATTATGTCAAAGCTGGCCGGAGAAAGTGAGAGCAATCTCAGAA
AGGCGTTTGAAGAGGCAGAGAAGAACGCGCCGGCCATCATCTTCATCGATGAGATTGATTCCATAGCCCCAAAGAGAGAC
AAGACCAACGGAGAGGTCGAAAGGCGTATTGTTTCGCAGCTGCTCACTCTTATGGACGGGCTTAAATCACGTGCCCATGT
TATTGTTATGGGTGCTACCAACCGCCCGAATAGCATCGACCCTGCTCTCAGAAGATTTGGTAGGTTTGACCGGGAGATCG
ACATTGGGGTCCCTGATGAAGTTGGACGGCTTGAGGTTCTCCGAATTCACACTAAAAACATGAAGCTAGCTGAAGATGTT
GAGCTGGAGCATGTTTCGAGGGACACTCATGGGTATGTCGGCGCTGATCTTGCTGCCCTTTGTACCGAGGCTGCTCTCCA
GTGCATCCGTGAGAAGATGGACGTTATAGACCTCGAGGATGACACCATTGATGCAGAGATACTGAATTCCATGGCTGTCA
CGAACGACCATTTCAAGATTGCGCTAGGGACAAGCAACCCATCTGCTCTTCGTGAGACCGTTGTCGAAGTTCCAAATGTC
TCTTGGGAGGATATTGGTGGCCTGGAGACCGTCAAAAAGGAGCTGCAGGAGACCGTCCAGTATCCGGTGGAGCATCCCGA
GAAATTTGAGAAGTTTGGTATGTCTCCCTCCAAAGGTGTTCTGTTCTATGGACCTCCGGGCTGTGGTAAGACCTTGTTGG
CCAAGGCAATTGCTAACGAGTGCCAGGCTAACTTTATCAGCATCAAAGGGCCAGAGTTGCTTACCATGTGGTTTGGTGAG
AGTGAGGCCAATGTGCGTGAGATTTTCGACAAGGCTAGGGGGTCAGCGCCATGCGTCCTCTTCTTTGACGAGCTTGACTC
AATTGCCACTCAGAGAGGAAACAGTGTTGGCGATGCCGGAGGTGCCGCCGATAGGGTGCTGAATCAGCTTCTTACCGAGA
TGGACGGGATGAATGCCAAG

Alignment

ORF - retro_hvul_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.24 %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPPQQGEPSSSADPKAKKDYSTAILERKKSPNRLVVDEATNDDNSVVALHPDTMERLQLFRGDTVLLKGK
          P....GEPSSS.DP..KKDYSTAILERKKSPNRLVVDEAT.DDNS.VALHPDT..RLQLF.GDT.LLKGK
Retrocopy PMAIHGEPSSS-DPSGKKDYSTAILERKKSPNRLVVDEATRDDNSAVALHPDTIDRLQLFTGDTLLLKGK

Parental  KRKDTICIVLADDTCDEPKVRMNKTVRKNLRVRLGDVVSVHQCPDVKYGKRVHILPIDDTVEGITGNLFD
          KRKDT.CI.L.DDTC...K.RMNK.VRKNLRVRLGDVVS.HQCPDVKYGKRVH.LPIDDTVEGI.GNLF.
Retrocopy KRKDTVCIALPDDTCEHTKIRMNKVVRKNLRVRLGDVVSIHQCPDVKYGKRVHVLPIDDTVEGIDGNLFE

Parental  AFLKPYFLEAYRPLRKGDLFLVRGGMRSVEFKVIETDPAEYCIVAPDTEIFCDGEPVKREDEERLDDVGY
          AFL.PYFLEAYRP.RKGDLFLVRGGM.SVEFKVIETDPAEYCIVAPDTEIFCDGEPV.REDEE.LDDVGY
Retrocopy AFLRPYFLEAYRPVRKGDLFLVRGGMTSVEFKVIETDPAEYCIVAPDTEIFCDGEPVRREDEEKLDDVGY

Parental  DDVGGVRKQMAQIRELVELPLRHPQLFKSIGVKPPKGILLFGPPGSGKTLIARAVANETGAFFFLINGPE
          DDVGGVRKQMAQIRELVELPLRHPQLFKSIGVKPPKGILL.GPPG.GKTLIARAVANETGAFFFLINGPE
Retrocopy DDVGGVRKQMAQIRELVELPLRHPQLFKSIGVKPPKGILLYGPPGTGKTLIARAVANETGAFFFLINGPE

Parental  IMSKLAGESESNLRKAFEEAEKNAPSIIFIDEIDSIAPKREKTNGEVERRIVSQLLTLMDGLKSRAHVIV
          IMSKLAGESESNLRKAFEEAEKNAP.IIFIDEIDSIAPKR.KTNGEVERRIVSQLLTLMDGLKSRAHVIV
Retrocopy IMSKLAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRIVSQLLTLMDGLKSRAHVIV

Parental  MGATNRPNSIDPALRRFGRFDREIDIGVPDEVGRLEVLRIHTKNMKLAEDVELEHISRDTHGYVGADLAA
          MGATNRPNSIDPALRRFGRFDREIDIGVPDEVGRLEVLRIHTKNMKLAEDVELEH.SRDTHGYVGADLAA
Retrocopy MGATNRPNSIDPALRRFGRFDREIDIGVPDEVGRLEVLRIHTKNMKLAEDVELEHVSRDTHGYVGADLAA

Parental  LCTEAALQCIREKMDIIDLEDETIDAEILNSMAVTNDHFKTALTTSNPSALRETVVEVPNVSWEDIGGLE
          LCTEAALQCIREKMD.IDLED.TIDAEILNSMAVTNDHFK.AL.TSNPSALRETVVEVPNVSWEDIGGLE
Retrocopy LCTEAALQCIREKMDVIDLEDDTIDAEILNSMAVTNDHFKIALGTSNPSALRETVVEVPNVSWEDIGGLE

Parental  NVKRELQETVQYPVEHPEKFEKFGMSPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFG
          .VK.ELQETVQYPVEHPEKFEKFGMSPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFG
Retrocopy TVKKELQETVQYPVEHPEKFEKFGMSPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFG

Parental  ESEANVREIFDKARGSAPCVLFFDELDSIATQRGSSVGDAGGAADRVLNQLLTEMDGMNAK
          ESEANVREIFDKARGSAPCVLFFDELDSIATQRG.SVGDAGGAADRVLNQLLTEMDGMNAK
Retrocopy ESEANVREIFDKARGSAPCVLFFDELDSIATQRGNSVGDAGGAADRVLNQLLTEMDGMNAK

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_38 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,