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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattccccttcgtccactcttcatacccaaatgtaatgggcgaagatgatttgccttcttttgtttttttactgataacctaccgatgatggggagcagATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAGGGCTGCCGGCCCCGGCCTTCTACTTCCCGTGACATCCACGACGGTCTGG

Basic information

species Zea mays
transcript GRMZM2G357972_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|50338840|gb|CO533966.1|CO533966
EST:     GCTACCGCGCCCTCGCCGATGCTATCCTCGAAGCCCGCGACCGGCCCCAG                         ATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAG
genomic: GCTACCGCGCCCTCGCCGATGCTATCCTCGAAGCCCGCGACCGGCCCCAGgtattcccct ... tggggagcagATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAG
EST: gi|211354036|gb|FL428925.1|FL428925
EST:     GCTACCGCGCCCTCGCCGATGCTATCCTCGAAGCCCGCGACCGGCCCCAG                         ATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAG
genomic: GCTACCGCGCCCTCGCCGATGCTATCCTCGAAGCCCGCGACCGGCCCCAGgtattcccct ... tggggagcagATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAG
EST: gi|78091875|gb|DV520249.1|DV520249
EST:     GCTACCGCGCCCTCGCCGATGCTATCCTCGAAGCCCGCGACCGGCCCCAG                         ATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAG
genomic: GCTACCGCGCCCTCGCCGATGCTATCCTCGAAGCCCGCGACCGGCCCCAGgtattcccct ... tggggagcagATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAG
EST: gi|31360546|gb|CD444903.1|CD444903
EST:     GCTACCGCGCCCTCGCCGATGCTATCCTCGAAGCCCGCGACCGGCCCCAG                         ATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAG
genomic: GCTACCGCGCCCTCGCCGATGCTATCCTCGAAGCCCGCGACCGGCCCCAGgtattcccct ... tggggagcagATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAG

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), 47 (downstream exon)
Score: 223

GAACCTCCTCCAGCTGTTCGATAACTCCTGGGAGCCCATTGAGGACGAGTGCTACCGCGCCCTCGCCGATGCTATCCTCGAAGCCCGCGACCGGCCCCAGgtattcccct ... tggggagcagATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAGGGCTGCCGGCCCCGGCCTTCTACTTCCCGTGACATCCACGACGGTCTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 62

GAACCTCCTCCAGCTGTTCGATAACTCCTGGGAGCCCATTGAGGACGAGTGCTACCGCGCCCTCGCCGATGCTATCCTCGAAGCCCGCGACCGGCCCCAGgtattcccct ... tggggagcagATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAGGGCTGCCGGCCCCGGCCTTCTACTTCCCGTGACATCCACGACGGTCTGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 46

GAACCTCCTCCAGCTGTTCGATAACTCCTGGGAGCCCATTGAGGACGAGTGCTACCGCGCCCTCGCCGATGCTATCCTCGAAGCCCGCGACCGGCCCCAGgtattcccct ... tggggagcagATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAGGGCTGCCGGCCCCGGCCTTCTACTTCCCGTGACATCCACGACGGTCTGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 113

GAACCTCCTCCAGCTGTTCGATAACTCCTGGGAGCCCATTGAGGACGAGTGCTACCGCGCCCTCGCCGATGCTATCCTCGAAGCCCGCGACCGGCCCCAGgtattcccct ... tggggagcagATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAGGGCTGCCGGCCCCGGCCTTCTACTTCCCGTGACATCCACGACGGTCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgatttgccttcttttgtttttttactgataacctaccgatgatggggagcagATGCATTGCAGCAACAGTACAAGAGGGGTTCGGCTTCCGCCGGAGGGGGAGGGCTGCCGGCCCCGGCCTTCTACTTCCCGTGACATCCACGACGGTCTGG
                            tgataac  putative branch site (score: 113)
           ttcttttgttttttta  TA-rich tract