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Clone: HW07C20

Genotype (Genotype)
  species: Hordeum vulgare
  type: wildtype
  common name: barley
  cultivar: Barke
Library:
  lib name: IPK_c2003
  tissue: roots
  stage/tissue: roots
  cloning vector: pBK-CMV site_1: EcoRI; site_2: XhoI
  host: XLOLR
  antibiotic: Kanamycin
  library description:
  mRNA was made from roots of spring barley variety 'Barke', a high quality malting variety. Roots were grown for two days on filter paper at room temperature Cloning sites: EcoRI (5'-end of cDNA) and XhoI (3'-end of cDNA). NOTE: Due to a cloning artefact caused by the kit, in most cases the EcoRIsite is NOT present, as well as the EcoRI adapter. Average insert size is 1 kb Sequence trimming: Vector sequences and sequence ends were trimmed from the 5'-and 3'-end until a 50 bp window contains less than two ambiguities. The maximum length was set to 700 bp

Related with
LOC_Os01g55830.1 annotated gene (TIGR5)
LOC_Os03g56790.1 annotated gene (TIGR5)
Hv.932 unigene cluster
Hv.3134 unigene cluster
Zm.81924 unigene cluster
Zm.9 unigene cluster
Os.97997 unigene cluster
Sof.20462 unigene cluster
Sbi.17905 unigene cluster
Sbi.14146 unigene cluster
Hv.3880 unigene cluster
Os.2813 unigene cluster
Zm.81385 unigene cluster
Sbi.18323 unigene cluster
Sof.18017 unigene cluster
Zm.93843 unigene cluster
LOC_Os01g55830.1 annotated gene (MSU 6.1)
LOC_Os03g56790.1 annotated gene (MSU 6.1)
 
Sequence: HW07C20u
submitter of sequence: Dr. Wolfgang Michalek
length: 692
priming: 3-prime
EBI-Id: HVUL03154
GenBankAc: AL502312
IPK CR-EST: HW07C20u
Sequence features and Clone alignments (BLAST):
Click for Menu

Gene structure   UTR    start codon    stop codon    exon-exon border 
Clone alignments   forward    reverse    start    stop 
Protein domains   domain       
Click on sequence features to obtain additional information.
 
HW07C20u
TTTTTTTTTT TTTTTTTTTA TCTGGGCACA ATTTATTATC AAACCAGAGC ACGGGAATGC         60
TCATTTAAGT ACAAGATTCG ACAGGATCGC AAGCACAAGC CTGAACATTC AACACCAGGA        120
CACATCACAA GAACACACAC TAGGAAAGGC ACACATCGGG GGTGACACAC CTCGGCTTAT        180
TTCGACGAAC AAGCCCCAGA AACTAAGATC ATGGCTTCAT CAGCGCAGCG ACCTTCTGGA        240
CGGACGGCCT CGTCAGCAGG TCAGTCCACC AGGCCTTCAC ATGCGGGTAA GCGTCAAACA        300
GAGATGCATA GGGTGTGGCC GCCAAGCACA GGGTGACAGA CGCATGGTTA AGGTCCGCAA        360
GGCTGAGGAA GTCTCCAGCC AGGTACTTGG ACTTGGTGAG CCGCGCCTCG TACACCGCCA        420
GCACGTTCTT GATCTTAACA AGGTTGTCGT CGATGACCTT CTGGTCAGTG GCTCCCCCAA        480
GCATAGGATG GATAAGGCAC TCGAAGAGAA TGGGGCTCAG AGCGGCGGTG TACTGATGGG        540
CCTCCACCTC GAGCCACACA TCCACCATTG CTGACTCCTT GATGTCGCCC TCCTTCAACA        600
AGCTCTGGCT TGTTCTTGCG GGACGCATAC TTGCAAATTA GCACGTGATT CGAANGACAT        660
TACAAAGTCC ACCATCCCTG CAAAAGGCTG GG                                      692
TypePositionOrientation
ORF 1 - 162: forward
ORF 2 - 571: forward
ORF 3 - 65: forward
ORF 64 - 2: reverse
ORF 125 - 42: reverse
ORF 211 - 333: forward
ORF 345 - 280: reverse
ORF 453 - 533: forward
ORF 628 - 212: reverse
ORF 690 - 598: reverse
Cluster Info:
Contig168.1 (88 members)
view Blast Searches
 
Sequence: HW07C20V
submitter of sequence: Dr. Wolfgang Michalek
length: 556
priming: 5-prime
EBI-Id: HVUL05872
GenBankAc: AL505030
IPK CR-EST: HW07C20V
Sequence features and Clone alignments (BLAST):
Click for Menu

Gene structure   UTR    start codon    stop codon    exon-exon border 
Clone alignments   forward    reverse    start    stop 
Protein domains   domain       
Click on sequence features to obtain additional information.
 
HW07C20V
ATCANCTAGA GCCATGCATA ACGGCCGAAT GATACGCTTT GCAGGAAACC TGGATATATN         60
TGTCTTATTA ACAACACTGT GGCAGCAGCA TTACCACGGA TGGCATGAAT TTGCATCCGA        120
CTGAAGCCCA CAGGTGATCA TCGGTCCGCC CTAGTGCGCC CGGTCACGGA GGACGTCAAG        180
CTCCACCTCG GTCGGGTCAG TTGCCTGGAT CTCGTAGTGG AACCCGTCGA GCTCTTGCTT        240
GATGCGGTCC TTGGAGGTGG AGTACAGCAT CTTGGCTCGG ATGCGGGATG TGTCAGGGGA        300
CCAGGCAATG AAGAAAATCT TGCTTTTCTG CACATTCTCC CCAGTAACAA AGTCAAAATC        360
ATAAAGCGCA TATCTGCAGT CGTTCTCTGG GAGACAAGCC AGGAAATCAT CATAACTCTC        420
AGTTGTAGCC CCTGTCTTCT CCACAACAAC CTGCTTTTGC TTTTCTTCTA TCTTGAAGAT        480
AACATAGCGA AATGCCTTCT TCATCTGAAG CTCCAGGAAA TGTCTCCCTG ATATCAGGAG        540
CCAACTCCCA TGCCAG                                                        556
TypePositionOrientation
ORF 2 - 121: forward
ORF 116 - 9: reverse
ORF 242 - 361: forward
ORF 413 - 141: reverse
ORF 492 - 554: forward
ORF 555 - 154: reverse
ORF 556 - 422: reverse
Cluster Info:
Contig472.1 (40 members)
view Blast Searches
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