Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagcactttcatgagagagtgttctctcttgatcacttgatctataacagagaatacgaaagaaaattgtcttatataatcaaacctttgaattctcagAGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG

Basic information

species Zea mays
transcript GRMZM2G052423_T01
intron # 2
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|110945900|gb|EE166057.1|EE166057
EST:     GTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAG                         AGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATT
genomic: GTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAGgtgattaggc ... gaattctcagAGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATT
EST: gi|60395139|gb|DN228008.1|DN228008
EST:     GTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAG                         AGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATT
genomic: GTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAGgtgattaggc ... gaattctcagAGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATT
EST: gi|60345305|gb|DN212278.1|DN212278
EST:     GTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAG                         AGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATT
genomic: GTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAGgtgattaggc ... gaattctcagAGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATT
EST: gi|211003125|gb|FL168897.1|FL168897
EST:     GTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAG                         AGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATT
genomic: GTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAGgtgattaggc ... gaattctcagAGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATT
EST: gi|211063518|gb|FL294403.1|FL294403
EST:     GTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAG                         AGGAGAGGTGGGGAAATGGATTGCGATTATTGCTGTTATTCTGCGCCTATT
genomic: GTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAGgtgattaggc ... gaattctcagAGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATT

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), 48 (downstream exon)
Score: 63

TGATATTGGACCGCACGAACTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAGgtgattaggc ... gaattctcagAGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 126

TGATATTGGACCGCACGAACTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAGgtgattaggc ... gaattctcagAGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 120

TGATATTGGACCGCACGAACTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAGgtgattaggc ... gaattctcagAGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG


Block sizes: 44 (upstream exon), 40 (downstream exon)
Score: 106

TGATATTGGACCGCACGAACTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACTCTGCCTAATGTGCTGTTTTCTCTGATCAGgtgattaggc ... gaattctcagAGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacagagaatacgaaagaaaattgtcttatataatcaaacctttgaattctcagAGGAGAGGTGGGGAAATGGATTGCGATTATTGCTCTTATTCTGCGCCTATTTTTTCCGCGCCACTTCCCAG
 ctataac  putative branch site (score: 106)
                                                ttctc  putative PPT
              aaagaaaattgtctta  TA-rich tract