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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgggacgaagagtatataagcaatcacttctgtcaaaattttgttcagttgtatataagcaatccatatatttgatacttatccattgctcttctgtagGCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG

Basic information

species Zea mays
transcript GRMZM2G105004_T01
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|31351435|gb|CD435792.1|CD435792
EST:     GATGCAGAGATGGACATTGTTTGCGATGCCTTGCAG                         GCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG
genomic: GATGCAGAGATGGACATTGTTTGCGATGCCTTGCAGgcaagttcta ... tcttctgtagGCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG
EST: gi|211052494|gb|FK991528.1|FK991528
EST:     AGAAACCTAATTTTGATGCAGAGATGGACATTGTTTGCGATGCCTTGCAG                         GCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG
genomic: AGAAACCTAATTTTGATGCAGAGATGGACATTGTTTGCGATGCCTTGCAGgcaagttcta ... tcttctgtagGCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG
EST: gi|211052496|gb|FK991530.1|FK991530
EST:     AGAAACCTAATTTTGATGCAGAGATGGACATTGTTTGCGATGCCTTGCAG                         GCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG
genomic: AGAAACCTAATTTTGATGCAGAGATGGACATTGTTTGCGATGCCTTGCAGgcaagttcta ... tcttctgtagGCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG
EST: gi|211052498|gb|FK991532.1|FK991532
EST:     AGAAACCTAATTTTGATGCAGAGATGGACATTGTTTGCGATGCCTTGCAG                         GCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG
genomic: AGAAACCTAATTTTGATGCAGAGATGGACATTGTTTGCGATGCCTTGCAGgcaagttcta ... tcttctgtagGCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG

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: 46 (upstream exon), 42 (downstream exon)
Score: 84

TCCCAGCAAGGGCTCTTGTTGTGCAGTTCTTGAACTTGTCACAAACAAGGAGAAACCTAATTTTGATGCAGAGATGGACATTGTTTGCGATGCCTTGCAGgcaagttcta ... tcttctgtagGCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG


Block sizes: 46 (upstream exon), 42 (downstream exon)
Score: 112

TCCCAGCAAGGGCTCTTGTTGTGCAGTTCTTGAACTTGTCACAAACAAGGAGAAACCTAATTTTGATGCAGAGATGGACATTGTTTGCGATGCCTTGCAGgcaagttcta ... tcttctgtagGCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 95

TCCCAGCAAGGGCTCTTGTTGTGCAGTTCTTGAACTTGTCACAAACAAGGAGAAACCTAATTTTGATGCAGAGATGGACATTGTTTGCGATGCCTTGCAGgcaagttcta ... tcttctgtagGCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 74

TCCCAGCAAGGGCTCTTGTTGTGCAGTTCTTGAACTTGTCACAAACAAGGAGAAACCTAATTTTGATGCAGAGATGGACATTGTTTGCGATGCCTTGCAGgcaagttcta ... tcttctgtagGCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagttgtatataagcaatccatatatttgatacttatccattgctcttctgtagGCTGTGAACTTGCAGACAACAACAGATCGCAGCAATCAGAAG
                         atttgat  putative branch site (score: 74)
                                     tccattgctcttct  putative PPT
                     atatatttgatactta  TA-rich tract