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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttaactggctaagcattgaatcatagcaataatatttcatacaatgtggcattgcaaactgcgttcaaccaaaactaacttgtggcctcgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCCTACAGGCAGAGGCAACAGCAACAGGTGTATGGTTCAGCAGTGCCTAATC

Basic information

species Zea mays
transcript GRMZM2G114513_T02
intron # 13
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|89759668|gb|DY688415.1|DY688415
EST:     TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTG                         GGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
genomic: TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
EST: gi|14203837|gb|BG837514.1|BG837514
EST:     TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTG                         GGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
genomic: TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
EST: gi|211478858|gb|FL037619.1|FL037619
EST:     TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTTGGTCAATTG                         GGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
genomic: TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
EST: gi|14203770|gb|BG837447.1|BG837447
EST:     TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTG                         GGTGGTGGATTTGACAAGCTCATTTTGGACAGCCCTTATGATGACGGGGCC
genomic: TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
EST: gi|211079576|gb|FL056322.1|FL056322
EST:     TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTTGGTCAATTG                         GGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
genomic: TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
EST: gi|16926672|gb|BM079740.1|BM079740
EST:     CTGTCGGTCAATTG                         GGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
genomic: CTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
EST: gi|89759667|gb|DY688414.1|DY688414
EST:     TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTG                         GGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
genomic: TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
EST: gi|6563789|gb|AW231321.1|AW231321
EST:     CCGAGCAAC-CGACTTCAT-TGCGTCTGTCGGTCAATTG                         GGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
genomic: CCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
EST: gi|60342431|gb|DN209404.1|DN209404
EST:     TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTG                         GGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC
genomic: TTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCC

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), 49 (downstream exon)
Score: 371

CACTGCATTTCAAGATAAGGGGTTTGATCCTACAGGATGGGAACTCGCCCTTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCCTACAGGCAGAGGCAACAGCAACAGGTGTATGGTTCAGCAGTGCCTAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

CACTGCATTTCAAGATAAGGGGTTTGATCCTACAGGATGGGAACTCGCCCTTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCCTACAGGCAGAGGCAACAGCAACAGGTGTATGGTTCAGCAGTGCCTAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

CACTGCATTTCAAGATAAGGGGTTTGATCCTACAGGATGGGAACTCGCCCTTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCCTACAGGCAGAGGCAACAGCAACAGGTGTATGGTTCAGCAGTGCCTAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

CACTGCATTTCAAGATAAGGGGTTTGATCCTACAGGATGGGAACTCGCCCTTGTTACCGCACCGAGCAACACGACTTCATCTGCGTCTGTCGGTCAATTGgtttgtttct ... cgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCCTACAGGCAGAGGCAACAGCAACAGGTGTATGGTTCAGCAGTGCCTAATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtggcattgcaaactgcgttcaaccaaaactaacttgtggcctcgttttacagGGTGGTGGATTTGACAAGCTCATTTTGGACAGCCTTTATGATGACGGGGCCTACAGGCAGAGGCAACAGCAACAGGTGTATGGTTCAGCAGTGCCTAATC
                             aactaac  putative branch site (score: 296)
                                          cctcgtttt  putative PPT
                           aaaactaa  TA-rich tract