RetrogeneDB ID: retro_hvul_29

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 2:490476141..490477155(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_3743
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_71584
• Aliases: None
• Description: None

Sequence

>retro_hvul_29
ATGGCCTCCTCAAGGTCTCTCAGCAGTCGCAGCGGCACAATGCTGGCCGGCGCGCTGCTCCTGCTACTGTGTGCGACCTC
CGCCGTGGCTCAGCTGGACGTTGGCTTCTACAGCAAGACGTGCCCGCACGTGGAGGAGATCGTCCGGCAGGAGATGCTAG
GGATCCTCAAGGAGGCTCCCACGCTCGCCGGACCCTTCCTCCGCCTCCACTTCCACGACTGCTTCGTCCGGGGATGCGAC
GCCTCCGTGCTGATCGACTCCACCGACGTCGCCAATAACCCAGCAGAGAAGGACGCGCCGCCCAACAAGAGCCTCCGCGG
CTTCGGCGCCGTGCAGCGCGTCAAGGACAGGCTCCAGTCCGCCTGTCCTAACACCGTGTCCTGCGCCGACGTGCTCGCCC
TCATGGCCCGCGACGCCGTCGTGCTCGCAGGAGGCCCCACGTGGCCCGTCGCGCTCGGCCGGAGGGACGGCCGCGTCTCC
ATCGCTAACGAGACAAACCAGCTTCCCCCACCCACCTCCAACTTCACCCGCCTCTCCAAGATGTTCGCCGCCAAGGGCCT
CGACGCCAAGGATATCGCTGTGCTCTCCGGTGGCCACACGCTCGGCACCGCGCGCTGCGTGTCCTTCACGGACCGGCTGT
ACAACTTCACCGGCGCCAACAACCCCGCCGACGTCGACCCGGCACTGGACGCCGGATACATGGCCAGGCTGAGGTCCCAG
TGCCGGAGCCTAGCCGACAACACCACGCTCGCAGAGATGGACCCCGGCAGCTTCCTCACCTTCGACGCCGGCTACTACCG
CCTCGTGGCAAAGCGCAGAGGAATCCTCCACTCGGACTCCGCGCTCCTGGAACACCCGACCACCAGGGCGTACGTCGAGC
GCCAGGCCACCGGCCTCTTCGCCGACGAGTTCTTCCGCGACTTCGCCGAGTCCATGGTCAAGATGGGCAACATCGGCGTG
CTCACCGGACAACAGGGCGAGATCAGGAGCAAGTGCTACGCCGTTAACAAATAA

Alignment

ORF - retro_hvul_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 86.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IAKGRGEKMGSRAVIVALLLAAVAATCARAQLHEKFYSESCPSVEDVVRKEMVRALSLAPSLAGPLLRMH
          .A..R.....S.......LL....AT.A.AQL...FYS..CP.VE..VR.EM...L..AP.LAGP.LR.H
Retrocopy MASSRSLSSRSGTMLAGALLLLLCATSAVAQLDVGFYSKTCPHVEEIVRQEMLGILKEAPTLAGPFLRLH

Parental  FHDCFVRGCDGSVLLDS---ANKTAEKDALPNQTLRGFGFVDRVKAAVEKACPDTVSCADVLALIARDAV
          FHDCFVRGCD.SVL.DS...AN..AEKDA.PN..LRGFG.V.RVK.....ACP.TVSCADVLAL.ARDAV
Retrocopy FHDCFVRGCDASVLIDSTDVANNPAEKDAPPNKSLRGFGAVQRVKDRLQSACPNTVSCADVLALMARDAV

Parental  WLSKGPFWAVPLGRRDGSVSISNETDALPPPTANITVLTQLFDAVNLDAKDLVVLSAAHTIGTSHCFSFS
          .L..GP.W.V.LGRRDG.VSI.NET..LPPPT.N.T.L...F.A..LDAKD..VLS..HT.GT..C.SF.
Retrocopy VLAGGPTWPVALGRRDGRVSIANETNQLPPPTSNFTRLSKMFAAKGLDAKDIAVLSGGHTLGTARCVSFT

Parental  DRLYNFTGMENASDIDPTLEPHYMMKLKSKCASLNDNTTLVEMDPGSFKTFDLDYFKLVSKRRGLFHSDG
          DRLYNFTG..N..D.DP.L...YM..L.S.C.SL.DNTTL.EMDPGSF.TFD..Y..LV.KRRG..HSD.
Retrocopy DRLYNFTGANNPADVDPALDAGYMARLRSQCRSLADNTTLAEMDPGSFLTFDAGYYRLVAKRRGILHSDS

Parental  ALLTHPVTRAYVQRHATGAFKEEFFADFAASMVKMGNANPLTGSQGEIRKKCSVVN
          ALL.HP.TRAYV.R.ATG.F..EFF.DFA.SMVKMGN...LTG.QGEIR.KC..VN
Retrocopy ALLEHPTTRAYVERQATGLFADEFFRDFAESMVKMGNIGVLTGQQGEIRSKCYAVN

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_29 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
Hordeum vulgare	MLOC_71584	1 retrocopy	retro_hvul_29 ,
Oryza glaberrima	ORGLA05G0189300	1 retrocopy	retro_ogla_25,
Triticum aestivum	Traes_4BL_4CC0E0AAA	1 retrocopy	retro_taes_34,