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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAGGGATTTGGGGGAACGAAGgtacccgatgcagcatacgtaccctttgcgaaagctaaaatctgatcgactagtcagtgaactccgctgttctgatttttactgagcatacatggtgcag

Basic information

species Zea mays
transcript GRMZM2G111954_T02
intron # 5
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|76281356|gb|DV020924.1|DV020924
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|149077171|gb|EE165834.2|EE165834
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|148931921|gb|EC875135.2|EC875135
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|148935240|gb|EC879277.2|EC879277
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|149063769|gb|EE157636.2|EE157636
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|67034494|gb|CO463044.1|CO463044
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGTCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|149013468|gb|EE042982.2|EE042982
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|148972626|gb|EE023587.2|EE023587
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|148982464|gb|EE028329.2|EE028329
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
EST: gi|148936271|gb|EC880349.2|EC880349
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCT
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCT
EST: gi|149111659|gb|EE190803.2|EE190803
EST:     TGGCCAGGGATTTGGGGGAACGAAG                         GATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG
genomic: TGGCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 2 RNA-Seq libraries.


Block sizes: 34 (upstream exon), 16 (downstream exon)
Score: 1

GCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG


Block sizes: 49 (upstream exon), 23 (downstream exon)
Score: 529

GCCAGGGATTTGGGGGAACGAAGgtacccgatg ... catggtgcagGATATCTTGATGGTCTCGCGGATGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG




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