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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGAAGGAAGGTGGTGTGGATGCCGTGCTCGTGTCTTCCTCTACAGGGATGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccctgtttctgcttatttatctctgtaccatactagcacttattaggttgtagcttgatagtttaggtactagtcttaaattttcttgctatta...

Basic information

species Zea mays
transcript GRMZM2G153386_T03
intron # 1
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|211321522|gb|FL287585.1|FL287585
EST:     TTCCTCACTGGGCTCCTTAGATTYGCCAACACGAAG                         ATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
genomic: TTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccct ... ttcctggcagATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
EST: gi|211321521|gb|FL287584.1|FL287584
EST:     TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAG                         ATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
genomic: TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccct ... ttcctggcagATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
EST: gi|211420279|gb|FL466289.1|FL466289
EST:     TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAG                         ATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
genomic: TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccct ... ttcctggcagATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
EST: gi|18171612|gb|BM341452.1|BM341452
EST:     TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAG                         ATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
genomic: TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccct ... ttcctggcagATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
EST: gi|18167887|gb|BM337727.1|BM337727
EST:     TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAG                         ATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
genomic: TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccct ... ttcctggcagATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
EST: gi|18165000|gb|BM334839.1|BM334839
EST:     TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAG                         ATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
genomic: TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccct ... ttcctggcagATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
EST: gi|16921912|gb|BM075348.1|BM075348
EST:     TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAG                         ATATCAAATGCAGAGTTTACATTTTCACCGTGAACACCTTTTCCTACCAAG
genomic: TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccct ... ttcctggcagATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG
EST: gi|18176861|gb|BM351794.1|BM351794
EST:     TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAG                         ATATCAAATGCAGAGTTTACATTTTCACCGTGGACACATTTTCCTACCAAG
genomic: TGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccct ... ttcctggcagATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAG

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: 47 (upstream exon), 36 (downstream exon)
Score: 8

CGGGAAGGAAGGTGGTGTGGATGCCGTGCTCGTGTCTTCCTCTACAGGGATGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccct ... ttcctggcagATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAGAGGTTATTACCAAGAATCCTCAATCCAAATCCAAGGCGTTCAGCATCAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 30

CGGGAAGGAAGGTGGTGTGGATGCCGTGCTCGTGTCTTCCTCTACAGGGATGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccct ... ttcctggcagATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAGAGGTTATTACCAAGAATCCTCAATCCAAATCCAAGGCGTTCAGCATCAT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 20

CGGGAAGGAAGGTGGTGTGGATGCCGTGCTCGTGTCTTCCTCTACAGGGATGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccct ... ttcctggcagATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAGAGGTTATTACCAAGAATCCTCAATCCAAATCCAAGGCGTTCAGCATCAT


Block sizes: 44 (upstream exon), 37 (downstream exon)
Score: 19

CGGGAAGGAAGGTGGTGTGGATGCCGTGCTCGTGTCTTCCTCTACAGGGATGCTCAGATTCCCCTTCCTCACTGGGCTCCTTAGATTCGCCAACACGAAGgtgcttccct ... ttcctggcagATATCAAATGCAGAGTTTACATTTTCACCGTGGACACCTTTTCCTACCAAGAGGTTATTACCAAGAATCCTCAATCCAAATCCAAGGCGTTCAGCATCAT