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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagatctagattgatttattactaaaccagtcttctagtattatacagagattgaagtatttctctctctttttcctaataatatatgtgcatatggcagAAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACATTGCATCCACTCGGAATCAATCAAGTTTGGACTTATCTAGTGAGGAAACCA

Basic information

species Zea mays
transcript GRMZM2G101412_T01
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|78106195|gb|DV524613.1|DV524613
EST:     GCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAG                         AAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACAGTGCATCCACTC
genomic: GCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAGgtattctgtg ... catatggcagAAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACATTGCATCCACTC
EST: gi|93281054|gb|EB673318.1|EB673318
EST:     GCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAG                         AAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAA-CAGTGCATCCACTC
genomic: GCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAGgtattctgtg ... catatggcagAAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACATTGCATCCACTC
EST: gi|76015302|gb|DT942472.1|DT942472
EST:     GCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAG                         AAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACAGTGCATCCACTC
genomic: GCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAGgtattctgtg ... catatggcagAAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACATTGCATCCACTC
EST: gi|78091707|gb|DV520081.1|DV520081
EST:     GCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAG                         AAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACAGTGCATCCACTC
genomic: GCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAGgtattctgtg ... catatggcagAAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACATTGCATCCACTC
EST: gi|76922300|gb|DV168931.1|DV168931
EST:     GCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCANAGAG                         AAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACAGTGCATCCACTC
genomic: GCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAGgtattctgtg ... catatggcagAAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACATTGCATCCACTC

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: 48 (upstream exon), 48 (downstream exon)
Score: 69

CGGGAGGAGCTGTCGCTGGTGCTGAAGCAGAAGGTTTATTATGATATTGCGCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAGgtattctgtg ... catatggcagAAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACATTGCATCCACTCGGAATCAATCAAGTTTGGACTTATCTAGTGAGGAAACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

CGGGAGGAGCTGTCGCTGGTGCTGAAGCAGAAGGTTTATTATGATATTGCGCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAGgtattctgtg ... catatggcagAAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACATTGCATCCACTCGGAATCAATCAAGTTTGGACTTATCTAGTGAGGAAACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

CGGGAGGAGCTGTCGCTGGTGCTGAAGCAGAAGGTTTATTATGATATTGCGCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAGgtattctgtg ... catatggcagAAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACATTGCATCCACTCGGAATCAATCAAGTTTGGACTTATCTAGTGAGGAAACCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 128

CGGGAGGAGCTGTCGCTGGTGCTGAAGCAGAAGGTTTATTATGATATTGCGCGGGGGCTGCACGAGTTGGGGGATAACAGCAGCCTCGCGCAGCAAAGAGgtattctgtg ... catatggcagAAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACATTGCATCCACTCGGAATCAATCAAGTTTGGACTTATCTAGTGAGGAAACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagagattgaagtatttctctctctttttcctaataatatatgtgcatatggcagAAGTGGTGGAATCATGGCGTGTTGAGAAGTTAAAAAACATTGCATCCACTCGGAATCAATCAAGTTTGGACTTATCTAGTGAGGAAACCA
                            tcctaat  putative branch site (score: 128)
                        tttttcctaataatat  TA-rich tract