RetrogeneDB ID: retro_hvul_12

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 1:157981054..157981981(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_43526
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_34709
• Aliases: None
• Description: None

Sequence

>retro_hvul_12
ATGGTTGTTCCGGTGATCGACTTCTCCAAGCTCGACGGCGCCGAGAGGGCGGAGACCATGGCGCAGATCGCCGACGGCTG
CGAGAACTGGGGGTTCTTCCAGCTGGTGAACCACGGCATCCCGCTGGAGCTTCTTGACCGCGTCAAGAAGGTGTGCTCCG
AGAGCTACCGCCTCCGCGAGGCGGCGTTCCGGTCGTCGAAGCCGGTGCAGACGCTGGAGAGGCTCGTGGAGGCGGAGCGG
CGCGGCGAGGCGGTGGCGCCGGTGGACGACATGGACTGGGAGGACATCTTCTACCTCCACGACAACAACCAGTGGCCTTC
CGATCCTCCGGCCTTCAAGGAGACCATGCGGGAGTACCGCTCCGAGCTCAAGAAGCTCGCGGAGCGGGTCATGGAGGCCA
TGGACGAGAACCTCGGGCTGGACAAGGGACGCATGAAGGCGGCCTTCACCGGCGACGGCCTCCACGCGCCATTCTTTGGC
ACTAAGGTCAGCCACTACCCGCCGTGCCCGCGCCCGGACCTCATCACCGGGCTCCGCGCCCACACCGACGCCGGCGGCGT
CATCCTGCTGTTCCAGGATGACAAGGTCGGGGGCCTTGAGGTGCTCAAGGATGGCCAGTGGCTGGACGTGCAGCCGCTCG
CCGACGCCATCGTGCTCAACACCGGCGACCAGGTGGAGGTGCTCAGCAACGGCCGCTACCGCAGCGCTTGGCACCGCGTC
CTGCCCATGCGCAACGGCAACCGCCGCTCCATCGCGTCCTTCTACAACCCGGCGTTCGAGGCGGCCATCTCGCCGGCGGT
GGGCGAAGGCGGCGCCGCCGCGTACCCGGACTACGTGTTCGGAGATTACATGGACGTGTACAACAAGCAGAAGTTCGATG
CCAAGGAGCCAAGATTCGAGGCCGTCAAGGCGCCGAAGTCAGCTTAA

Alignment

ORF - retro_hvul_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.9 %
• Parental protein coverage: 99.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAIPVIDFSRLDGDERAAALAEIAAGFEEWGFFQLVNTGIPDELLERVKKVCNDCYKLREEGFNGSNPAV
          M..PVIDFS.LDG.ERA...A.IA.G.E.WGFFQLVN.GIP.ELL.RVKKVC...Y.LRE..F..S.P.V
Retrocopy MVVPVIDFSKLDGAERAETMAQIADGCENWGFFQLVNHGIPLELLDRVKKVCSESYRLREAAFRSSKP-V

Parental  KALAALVEQEGEGLAPRKVQGMDWEDVFTLHDNLPWPSIPPTFKETMMEYRTELKKLAEKMLGVMEELLG
          ..L..LVE.E..G.A...V..MDWED.F.LHDN..WPS.PP.FKETM.EYR.ELKKLAE.....M.E.LG
Retrocopy QTLERLVEAERRGEAVAPVDDMDWEDIFYLHDNNQWPSDPPAFKETMREYRSELKKLAERVMEAMDENLG

Parental  LEEGQITKVFSKDGDFEPFYGTKVSHYPPCPRPEMVDGLRAHTDAGGLILLFQDDRVGGLQVLGRDGRWA
          L..G.....F..DG...PF.GTKVSHYPPCPRP....GLRAHTDAGG.ILLFQDD.VGGL.VL..DG.W.
Retrocopy LDKGRMKAAFTGDGLHAPFFGTKVSHYPPCPRPDLITGLRAHTDAGGVILLFQDDKVGGLEVL-KDGQWL

Parental  DVQPVENAIVINTGDQIEVMSNGRYKSAWHRVLATRDGNRRSIASFYNPARAATIAPAIPAAADSGPGGD
          DVQP...AIV.NTGDQ.EV.SNGRY.SAWHRVL..R.GNRRSIASFYNPA..A.I.PA.......G....
Retrocopy DVQPLADAIVLNTGDQVEVLSNGRYRSAWHRVLPMRNGNRRSIASFYNPAFEAAISPAV----GEGGAAA

Parental  YPSFSFGDYMEVYIKQKFQDKEPRFAAAAAIKN
          YP...FGDYM.VY.KQKF..KEPRF.A..A.K.
Retrocopy YPDYVFGDYMDVYNKQKFDAKEPRFEAVKAPKS

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_12 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_09413	1 retrocopy	retro_atau_21,
Hordeum vulgare	MLOC_34709	1 retrocopy	retro_hvul_12 ,