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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactaagctaaatcatcagtttactctcttgcctgtcttatcttggcatgttgatttcactgacagccttgtcttgtctctgtctgtttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAACCTGTGCACCCAGCAAACGCTGGCCCTGTCGTCCTTCCAACGCAGCCCAG

Basic information

species Zea mays
transcript GRMZM2G363460_T05
intron # 3
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|148971702|gb|EE022431.2|EE022431
EST:     GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGG                         TCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
genomic: GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
EST: gi|33468109|gb|CF245158.1|CF245158
EST:     GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGG                         TCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
genomic: GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
EST: gi|148946560|gb|EC885619.2|EC885619
EST:     GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGG                         TCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
genomic: GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
EST: gi|211174721|gb|FL404361.1|FL404361
EST:     GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGG                         TCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
genomic: GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
EST: gi|148947997|gb|EC893497.2|EC893497
EST:     GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGG                         TCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
genomic: GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
EST: gi|67019556|gb|CO448305.1|CO448305
EST:     GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGG                         TCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
genomic: GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
EST: gi|148941345|gb|EC886254.2|EC886254
EST:     GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGG                         TCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
genomic: GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
EST: gi|149085990|gb|EE175517.2|EE175517
EST:     GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGG                         TCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
genomic: GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
EST: gi|78109256|gb|DV527672.1|DV527672
EST:     GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGG                         TCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
genomic: GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
EST: gi|76913179|gb|DV165031.1|DV165031
EST:     GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGG                         TCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
genomic: GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
EST: gi|148980471|gb|EE027160.2|EE027160
EST:     GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGG                         TCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC
genomic: GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAAC

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), 47 (downstream exon)
Score: 50

GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAACCTGTGCACCCAGCAAACGCTGGCCCTGTCGTCCTTCCAACGCAGCCCAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 99

GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAACCTGTGCACCCAGCAAACGCTGGCCCTGTCGTCCTTCCAACGCAGCCCAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 159

GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAACCTGTGCACCCAGCAAACGCTGGCCCTGTCGTCCTTCCAACGCAGCCCAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 68

GATCCTCAACCCAGCACTACGGCTACCACTTCTCCGCAGCAGCAGGgtaactaagc ... ttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAACCTGTGCACCCAGCAAACGCTGGCCCTGTCGTCCTTCCAACGCAGCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggcatgttgatttcactgacagccttgtcttgtctctgtctgtttgcttacagTCAACAGCCAGAATCAATCCGTCGGGGTGCAAGCTTATGCGCCAGCACAACCTGTGCACCCAGCAAACGCTGGCCCTGTCGTCCTTCCAACGCAGCCCAG
               cactgac  putative branch site (score: 68)
                                        tctgttt  putative PPT
        ttgattt  TA-rich tract