RetrogeneDB ID: retro_hvul_70

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 4:447587876..447589058(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_58863
• Aliases: None
• Description: None

Sequence

>retro_hvul_70
ATGTCGGTCTTAATCGTCACCAGCGTGGGCGATCTCGTGGTGGATCTCCACACCGATCGGTGCCCCCGCACCACCTACAA
CTTCCTCAAGCTCTGCAAGATGAAGTACTACAACGGGTGCCTGTTCCACAAGGTGGCCAAGGATTTCGTGGCACAGACCG
GGGACCCGACCGGGACCGGGACTGGCGGCGATTCGGTGTACAAGTTCCTCCACGGTGATCAGGCTCGATTCTTCGACGAC
GAGATCCACCCGGAACTGAGGCATTCGAAGATCGGCACCGTTGCCATGGCAAGCGCCGGCAAAAACCGCAACGCCGCGCA
GTTCTACATCACACTGCGGGACGACGTGGAATACCTTATGATAAACACACCGTGTTTGGGATAGTTGCTGAAGGTGAAGG
TCTTGACACGCTGACGAAGATAAACGAATCATATGTTGATGGCGATGGGAGACCATTCAAGGACATAAGGATTAAACATA
CATGTGTCTTGTACGACCCTGACGACGATCCTGCCCAGCTTGCTGAACTCATTCCTGCAAATTCTCCCGTTGGAAAGCCA
ATCGAGGAGATTTCAGAAGAGCGCTTAGAGGATACCTGGGTCCCTCTCGATGAAACAGTGGACCCTGTGCAGCTTGAGGG
GATGATCCGTTCGAAAGAAGCGCATACAAATGCCGTGATCCTTGCTAGTATTGGAGACATTCCAGATGCCGAGGTCAAGC
CACCAGACAATGTCTTGTTTGTCTGTCAACTCAACCCACTGACACAGGATGAGGACCTGTATACGATATTTTCTCGCTTC
GGAACGGTGACATCGGCCGAAACAATCCGTGACTACAAGACTGATCACAGCTTGTGCTATGCTTTTGTTGAGTTCGAAGC
AAAGGAAGCCTGCGAGCGTGCACACAGGGATATGAACAATTGTCTGATTGATGACCGGAGAATTCAAGTTGATTTTAGCC
AGAGCGTTTCAAAGCTGTGGCGTCAGTTCAGACAGGGCACTCGGAATGCAAATAAAGATGGGTGCTGCAAGAGTCATGCC
CCTGATTATCGAGCCCGAGATCGGGATAAGGGTGCTGAGAAGAAAAACAAAGGACCGAGATTATGTTCTGAAAGATGAAA
ACACTCAGCTAGGCGGCAGTAAACGTGGAAGTTATGATTTAGTCTTTGATGAGGACGGTGCT

Alignment

ORF - retro_hvul_70 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.28 %
• Parental protein coverage: 70.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSVLIVTSVGDIELDLHTDLCPLTTKNFLKLCKMKYYNGCLFHKVEKDFLAQSGDPTGTGSGGDSVYKFL
          MSVLIVTSVGD...DLHTD.CP.TT.NFLKLCKMKYYNGCLFHKV.KDF.AQ.GDPTGTG.GGDSVYKFL
Retrocopy MSVLIVTSVGDLVVDLHTDRCPRTTYNFLKLCKMKYYNGCLFHKVAKDFVAQTGDPTGTGTGGDSVYKFL

Parental  YGDQARFFNDEIRPELRHSKTGTIAMASAGENCNASQFYITLRDDVDYLD-DKHTVFGTVAEG--LDTLT
          .GDQARFF.DEI.PELRHSK.GT.AMASAG.N.NA.QFYITLRDDV.YL..DKHTVFG.VAEG..LDTLT
Retrocopy HGDQARFFDDEIHPELRHSKIGTVAMASAGKNRNAAQFYITLRDDVEYLM<DKHTVFGIVAEGEGLDTLT

Parental  KINEAYVDDKGRPFKDIRIKHTYILDDPFDDPPQLAEFIPENSPLGKPHDEVAEERLEDSWVPLDETVDP
          KINE.YVD..GRPFKDIRIKHT..L.DP.DDP.QLAE.IP.NSP.GKP..E..EERLED.WVPLDETVDP
Retrocopy KINESYVDGDGRPFKDIRIKHTCVLYDPDDDPAQLAELIPANSPVGKPIEEISEERLEDTWVPLDETVDP

Parental  GQLEELIRSKEAHANAVILESVGDIPDAEVKPPDNVLFVCKLNPVTQDEDLYTIFSRFGSVTSAEIIRDF
          .QLE..IRSKEAH.NAVIL.S.GDIPDAEVKPPDNVLFVC.LNP.TQDEDLYTIFSRFG.VTSAE.IRD.
Retrocopy VQLEGMIRSKEAHTNAVILASIGDIPDAEVKPPDNVLFVCQLNPLTQDEDLYTIFSRFGTVTSAETIRDY

Parental  KTGDSLCYAFIEFEAKEACERAYFKMDNCLIDDRRIHVDFSQSVSKLWGQFRQSKRNGNKDGCFKCGAPD
          KT..SLCYAF.EFEAKEACERA...M.NCLIDDRRI.VDFSQSVSKLW.QFRQ..RN.NKDGC.K..APD
Retrocopy KTDHSLCYAFVEFEAKEACERAHRDMNNCLIDDRRIQVDFSQSVSKLWRQFRQGTRNANKDGCCKSHAPD

Parental  HIARDCDQDGEQKPKAP-NYVLKDDNTQRGGNNRRSYDFVFEDDTA
          ..ARD.D...E.K.K.P..YVLKD.NTQ.GG..R.SYD.VF..D.A
Retrocopy YRARDRDKGAEKKNKGP>DYVLKDENTQLGGSKRGSYDLVFDEDGA

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_70 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
Brachypodium distachyon	BRADI1G20760	1 retrocopy	retro_bdis_34,
Aegilops tauschii	F775_03869	1 retrocopy	retro_atau_2,
Hordeum vulgare	MLOC_58863	1 retrocopy	retro_hvul_70 ,