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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccgcttcgcttcggcttgcgttcttgcactcctggtgcttattttggggaattttttttcacctgagtttgtgatgagcgcagATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGGGGAGGCTAGGGGTTAGGATTCCGGCGTGATGCAGCGCCCGGGACGACTT

Basic information

species Zea mays
transcript GRMZM2G113453_T01
intron # 1
splice site 3'
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|211179215|gb|FL123985.1|FL123985
EST:     TCGCGATTCCGCTGGAGACTGTTCAGCTCCTCGCCGGCGGCGCTGATTCG                         ATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCWCTGGGAGCCGAGGG
genomic: TCGCGATTCCGCTGGAGACTGTTCAGCTCCTCGCCGGCGGCGCTGATTCGgtaccgcttc ... atgagcgcagATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGG
EST: gi|71765900|gb|DR963837.1|DR963837
EST:     TCGCGATTCCGCTGGAGACTGTTCAGCTCCTCGCCGGCGGCGCTGATTCG                         ATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGG
genomic: TCGCGATTCCGCTGGAGACTGTTCAGCTCCTCGCCGGCGGCGCTGATTCGgtaccgcttc ... atgagcgcagATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGG
EST: gi|149108986|gb|EE293082.2|EE293082
EST:     TCGCGATTCCGCTGGAGACTGTTCAGCTCCTCGCCGGCGGCGCTGATTCG                         ATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGG
genomic: TCGCGATTCCGCTGGAGACTGTTCAGCTCCTCGCCGGCGGCGCTGATTCGgtaccgcttc ... atgagcgcagATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGG
EST: gi|148973278|gb|EE024359.2|EE024359
EST:     TCGCGATTCCGCTGGAGACTGTTCAGCTCCTCGCCGGCGGCGCTGATTCG                         ATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGG
genomic: TCGCGATTCCGCTGGAGACTGTTCAGCTCCTCGCCGGCGGCGCTGATTCGgtaccgcttc ... atgagcgcagATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

GCCACACTCCCCAGAGGTTCTGAACGCAGATCTCTCGCCGCAGCTCGGCCTCGCGATTCCGCTGGAGACTGTTCAGCTCCTCGCCGGCGGCGCTGATTCGgtaccgcttc ... atgagcgcagATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGGGGAGGCTAGGGGTTAGGATTCCGGCGTGATGCAGCGCCCGGGACGACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 41

GCCACACTCCCCAGAGGTTCTGAACGCAGATCTCTCGCCGCAGCTCGGCCTCGCGATTCCGCTGGAGACTGTTCAGCTCCTCGCCGGCGGCGCTGATTCGgtaccgcttc ... atgagcgcagATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGGGGAGGCTAGGGGTTAGGATTCCGGCGTGATGCAGCGCCCGGGACGACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 25

GCCACACTCCCCAGAGGTTCTGAACGCAGATCTCTCGCCGCAGCTCGGCCTCGCGATTCCGCTGGAGACTGTTCAGCTCCTCGCCGGCGGCGCTGATTCGgtaccgcttc ... atgagcgcagATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGGGGAGGCTAGGGGTTAGGATTCCGGCGTGATGCAGCGCCCGGGACGACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

GCCACACTCCCCAGAGGTTCTGAACGCAGATCTCTCGCCGCAGCTCGGCCTCGCGATTCCGCTGGAGACTGTTCAGCTCCTCGCCGGCGGCGCTGATTCGgtaccgcttc ... atgagcgcagATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGGGGAGGCTAGGGGTTAGGATTCCGGCGTGATGCAGCGCCCGGGACGACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcctggtgcttattttggggaattttttttcacctgagtttgtgatgagcgcagATCTGACGCCCACGCAGCAGAAGGCTGAAGGAGGGCACTGGGAGCCGAGGGGGAGGCTAGGGGTTAGGATTCCGGCGTGATGCAGCGCCCGGGACGACTT
                     aattttttttca  TA-rich tract