RetrogeneDB ID: retro_hvul_51

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 2:22769360..22771013(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_36515
• Aliases: None
• Description: None

Sequence

>retro_hvul_51
ATGGACAATGGAATTGGACCGGTGGACGGGCACAAGGCGGTGTCGAACGGCGTGGTGGCGTGCCCCGTGGCATTCCGCGC
ATTGTCATCGCCGGCGGCGGCCACGGTCACCTCCGCCGAAGCCACGCTGGGCCGCCACCTTGCGCGGCGGCTGGTGGAGG
TGGGCGTGAGCGACGTGTTCGCCGTGCCGGGGGACTTCAACCTGGCCTTCCTCGACCACCTCATCGCCGAGCCCGGGCTG
CGCCTCGTCGGCTGCTGCAACGAGCTCAACGCCGGCTATGCGGCCGACGGGTACGCGCGCGCCAGGGGCGTGGGCGCCTG
CGCCGTCACGTTCACCGTCGGCGGGCTCAGCGTGCTCAACGCCATCGCCGGCGCCTACAGCGAGAACCTCCCCGTGATCT
GCATCGTCGGCGGGCCCAACTCCAACGACCACGGCACCAATCGCATCCTCCACCACACCATCGGCCTCCCCGACTTCTCC
CAGGAGCTCCGCTGCTTCCAGCCCGTCACCTGCCACCAGGTCGTCATCAACAACCTCGACGACGCCCACGAGCAGGTCGA
CAAGGCCATCGCCACGGCTCTCAGGGAGAGCAAGCCCGTCTACATCAGCATCGCCTGCAACCTCCCCGGCGTCTCCCACC
CGACCTTCTTCCGCGACCCCGTCCCCTACTGCCTCGACCCGCGGCTGAGCAACAAGATGGGACTCGAGGCGGCGCTGGAG
GCCACGGTGGAGTTCCTCAACAAAGCTGTAAAGCCGGTGATGGTGGCGGGGCCGAAGCTCCGGGTGGCCAAAGCAGCCGC
GGCGTTCGCGGAGCTGGCGGACGCGAGCGGGTACGCGGTGGCGACGATGCCGTCAGCGAAGGGGCTGGTGCCGGAGACGC
TGCCGCGGTTCATCGGCACCTACTGGGGCGCGGTGAGCACGCCCTTCTGCGCCGAGATCGTGGAGTCGGCGGACGCCTAC
CTCTTCGCCGGCCCCATCTTCAACGACTACAGCTCGGTGGGGTACTCGTTCCTGCTCAAGAAGGAGAAGGCGGTGATCGT
GCAGCCCGACCGCGTCACCGTCGGCGACGGCCCGACGTTCGGGTGCGTCATGATGAAGGACTTCCTGTCGGAGCTGGCCA
AGCGCATGAGCAACAAGAGGAACACCACGGCGCACGACAACTACCGTAGGATATTCGTGCCGCAGGGGCAGCCGCCGGAG
AGCGATCCCGGCGAGCCGCTGCGCGTCAACGTGCTATTCAAGCACATCCAGAAGATGCTCACCGGCGACAGCGCCGTCAT
CGCCGAGACCGGCGACTCGTGGTTCAACTGCCAGAAGCTCAAGCTGCCGGACGGCTGCGGGTACGAGTTCCAGATGCAGT
ACGGGTCCATCGGGTGGTCGGTGGGGGCGCTGCTCGGGTACGCGCAGGGAGCCGCCGGAGACAAGCGCCTGATCGCCTGC
ATCGGCGACGGGAGCTTCCAGGTGACGGCGCAGGACGTGTCGACGATGCTGCGGTGCCAGCAGAAGAGCATCATCTTCCT
CCTCAACAACGGCGGGTACACCATCGAGGTGGAGATCCACGACGGGCCATACAACGTCATCAAGAACTGGAACTACACGG
GGCTCGTCGACGCCATCCACAACGGCGAGGGCAACTGCTGGACCGCAAAGGTA

Alignment

ORF - retro_hvul_51 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 90.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  METGIGSVDGPKGAPSGAVACPATFPA-SSPTF--IGSPEATLGRHLARRLVQIGVGDVFAVPGDFNLTL
          M..GIG.VDG.K....G.VACP..F.A.SSP......S.EATLGRHLARRLV..GV.DVFAVPGDFNL..
Retrocopy MDNGIGPVDGHKAVSNGVVACPVAFRALSSPAAATVTSAEATLGRHLARRLVEVGVSDVFAVPGDFNLAF

Parental  LDHLIAEPRLRLVGCCNELNAGYAADGYARARGVGACAVTFTVGGLSVLNAIAGAYSENLPLICIVGGPN
          LDHLIAEP.LRLVGCCNELNAGYAADGYARARGVGACAVTFTVGGLSVLNAIAGAYSENLP.ICIVGGPN
Retrocopy LDHLIAEPGLRLVGCCNELNAGYAADGYARARGVGACAVTFTVGGLSVLNAIAGAYSENLPVICIVGGPN

Parental  SNDYGTNRVLHHTIGLPDFSQELRCFTPVTCYQAVVNNLEDAHEQIDKAISTALKESKPVYISVSCNLPG
          SND.GTNR.LHHTIGLPDFSQELRCF.PVTC.Q.V.NNL.DAHEQ.DKAI.TAL.ESKPVYIS..CNLPG
Retrocopy SNDHGTNRILHHTIGLPDFSQELRCFQPVTCHQVVINNLDDAHEQVDKAIATALRESKPVYISIACNLPG

Parental  VPHPTFSRDPVPYFLAPRMSNQMGLEAAVEATVAFLDKAVKPVMVAGPKLRVAKAGAAFAELADASGYAV
          V.HPTF.RDPVPY.L.PR.SN.MGLEAA.EATV.FL.KAVKPVMVAGPKLRVAKA.AAFAELADASGYAV
Retrocopy VSHPTFFRDPVPYCLDPRLSNKMGLEAALEATVEFLNKAVKPVMVAGPKLRVAKAAAAFAELADASGYAV

Parental  ATMPSAKGLVAETLPRFIGTYWGAVSTAFCSEIVESSDAYLFAGPIFNDYSSVGYSFLLKKEKAVIVQPD
          ATMPSAKGLV.ETLPRFIGTYWGAVST.FC.EIVES.DAYLFAGPIFNDYSSVGYSFLLKKEKAVIVQPD
Retrocopy ATMPSAKGLVPETLPRFIGTYWGAVSTPFCAEIVESADAYLFAGPIFNDYSSVGYSFLLKKEKAVIVQPD

Parental  RVTVGNGPAFGCIMMKDFLGELSKRL--KKNTTAYENYKRIWVPEGQPPESEPGEPLRVNVLFKHVQKML
          RVTVG.GP.FGC.MMKDFL.EL.KR...K.NTTA..NY.RI.VP.GQPPES.PGEPLRVNVLFKH.QKML
Retrocopy RVTVGDGPTFGCVMMKDFLSELAKRMSNKRNTTAHDNYRRIFVPQGQPPESDPGEPLRVNVLFKHIQKML

Parental  TGDSAVIAETGDSWFNCQKLKLPDGCGYEFQMQYGSIGWSVGALLGYAQGAR-DKRVIACIGDGSFQVTA
          TGDSAVIAETGDSWFNCQKLKLPDGCGYEFQMQYGSIGWSVGALLGYAQGA..DKR.IACIGDGSFQVTA
Retrocopy TGDSAVIAETGDSWFNCQKLKLPDGCGYEFQMQYGSIGWSVGALLGYAQGAAGDKRLIACIGDGSFQVTA

Parental  QDVSTMLRCEQNSIIFLINNGGYTIEVEIHDGPYNVIKNWNYTGLVDAIHNGEGKCWTAKV
          QDVSTMLRC.Q.SIIFL.NNGGYTIEVEIHDGPYNVIKNWNYTGLVDAIHNGEG.CWTAKV
Retrocopy QDVSTMLRCQQKSIIFLLNNGGYTIEVEIHDGPYNVIKNWNYTGLVDAIHNGEGNCWTAKV

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_51 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_36515	1 retrocopy	retro_hvul_51 ,