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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accaaacttagtccgtcttgttgctgcaaattcccgtctttcgatctataatatcgctcacggcaactgctattttccccgcctgtggtcgttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAACAGCCCGCAAGTGCCCAACGGCGTGTTGCGGCCCACCGTGTCTTCCTCC

Basic information

species Zea mays
transcript GRMZM2G040017_T02
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|211042422|gb|FL285126.1|FL285126
EST:     GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAG                         ACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
genomic: GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
EST: gi|148975629|gb|EE025759.2|EE025759
EST:     GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAG                         ACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTTCAAGGTCA
genomic: GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTT-CAAGGTCA
EST: gi|211045384|gb|FL285133.1|FL285133
EST:     CTGACCCCCGCCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAG                         ACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
genomic: CTGACCCCCGCC-ATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
EST: gi|71769706|gb|DR967643.1|DR967643
EST:     GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAG                         ACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
genomic: GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
EST: gi|149075133|gb|EE163627.2|EE163627
EST:     GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAG                         ACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
genomic: GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
EST: gi|211042420|gb|FL285124.1|FL285124
EST:     CTGACCCCCGCCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAG                         ACTTATGATGATGGAGACCC-TCAAATCGAGATGGGCGGTTTCAAGGTCAA
genomic: CTGACCCCCGCC-ATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
EST: gi|149072532|gb|EE160814.2|EE160814
EST:     GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAG                         ACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
genomic: GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
EST: gi|89760510|gb|DY688889.1|DY688889
EST:     GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAG                         ACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
genomic: GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
EST: gi|211042419|gb|FL285123.1|FL285123
EST:     CTGACCCCCGCCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAG                         ACTTATGATGATGGA
genomic: CTGACCCCCGCC-ATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGA
EST: gi|91867362|gb|EB399659.1|EB399659
EST:     GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAG                         ACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
genomic: GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
EST: gi|149085154|gb|EE174658.2|EE174658
EST:     GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAG                         ACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA
genomic: GCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAA

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), 46 (downstream exon)
Score: 42

TTCCTAGGGAGCCGTGGCGGCCGGAGCACCCTTCCAACTCCTGATCCCGAGCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAACAGCCCGCAAGTGCCCAACGGCGTGTTGCGGCCCACCGTGTCTTCCTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 50

TTCCTAGGGAGCCGTGGCGGCCGGAGCACCCTTCCAACTCCTGATCCCGAGCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAACAGCCCGCAAGTGCCCAACGGCGTGTTGCGGCCCACCGTGTCTTCCTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 27

TTCCTAGGGAGCCGTGGCGGCCGGAGCACCCTTCCAACTCCTGATCCCGAGCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAACAGCCCGCAAGTGCCCAACGGCGTGTTGCGGCCCACCGTGTCTTCCTCC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 59

TTCCTAGGGAGCCGTGGCGGCCGGAGCACCCTTCCAACTCCTGATCCCGAGCTGACCCCCGCCATCGCAGCGGCGGCTCTGCCGCAGCGTCTGTGTCCAGgtgaggttgg ... gttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAACAGCCCGCAAGTGCCCAACGGCGTGTTGCGGCCCACCGTGTCTTCCTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctataatatcgctcacggcaactgctattttccccgcctgtggtcgttgtcgtagACTTATGATGATGGAGACCCCTCAAATCGAGATGGGCGGTTTCAAGGTCAACAGCCCGCAAGTGCCCAACGGCGTGTTGCGGCCCACCGTGTCTTCCTCC
         cgctcac  putative branch site (score: 59)
                         tatttt  TA-rich tract