Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatcatacgcagttgggtctatccatctgtcactgtctgaacaagttctgtcctctaatagtgctatggttggctcactcatttgcttttattttgtttgttctactttttttttactaattataacacatgttttctaaccgattgcccccacagAAAATGAGGAACAATCGGAAACGTCGCTCGCTCTGGCTGAGGTAACTGAAAAGGCACTGAGCATCCAAAACCAGCACAACGACGCTGTCCTTTACCAAGG

Basic information

species Zea mays
transcript AC217358.3_FGT003
intron # 9
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|60396473|gb|DN229342.1|DN229342
EST:     ACGCTTTTCTTTTATCAAAGGTGTCTATGTGGAAGATAATTGCCCTCAAG                         AAAATGAGGAACAATCGGAAACGTCGCTCGCTCTGGCTGAGGTAACTGAAA
genomic: ACGCTTTTCTTTTATCAAAGGTGTCTATGTGGAAGATAATTGCCCTCAAGgtacatcata ... gcccccacagAAAATGAGGAACAATCGGAAACGTCGCTCGCTCTGGCTGAGGTAACTGAAA




















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: 41 (upstream exon), 47 (downstream exon)
Score: 29

GATTTGATCACTTCAGAGAAACAAGAAGCTGCGAGCACAACAGGAGAAGCACGCTTTTCTTTTATCAAAGGTGTCTATGTGGAAGATAATTGCCCTCAAGgtacatcata ... gcccccacagAAAATGAGGAACAATCGGAAACGTCGCTCGCTCTGGCTGAGGTAACTGAAAAGGCACTGAGCATCCAAAACCAGCACAACGACGCTGTCCTTTACCAAGG


Block sizes: 16 (upstream exon), 44 (downstream exon)
Score: 8

GATTTGATCACTTCAGAGAAACAAGAAGCTGCGAGCACAACAGGAGAAGCACGCTTTTCTTTTATCAAAGGTGTCTATGTGGAAGATAATTGCCCTCAAGgtacatcata ... gcccccacagAAAATGAGGAACAATCGGAAACGTCGCTCGCTCTGGCTGAGGTAACTGAAAAGGCACTGAGCATCCAAAACCAGCACAACGACGCTGTCCTTTACCAAGG


Block sizes: 34 (upstream exon), 46 (downstream exon)
Score: 9

GATTTGATCACTTCAGAGAAACAAGAAGCTGCGAGCACAACAGGAGAAGCACGCTTTTCTTTTATCAAAGGTGTCTATGTGGAAGATAATTGCCCTCAAGgtacatcata ... gcccccacagAAAATGAGGAACAATCGGAAACGTCGCTCGCTCTGGCTGAGGTAACTGAAAAGGCACTGAGCATCCAAAACCAGCACAACGACGCTGTCCTTTACCAAGG


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 10

GATTTGATCACTTCAGAGAAACAAGAAGCTGCGAGCACAACAGGAGAAGCACGCTTTTCTTTTATCAAAGGTGTCTATGTGGAAGATAATTGCCCTCAAGgtacatcata ... gcccccacagAAAATGAGGAACAATCGGAAACGTCGCTCGCTCTGGCTGAGGTAACTGAAAAGGCACTGAGCATCCAAAACCAGCACAACGACGCTGTCCTTTACCAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctactttttttttactaattataacacatgttttctaaccgattgcccccacagAAAATGAGGAACAATCGGAAACGTCGCTCGCTCTGGCTGAGGTAACTGAAAAGGCACTGAGCATCCAAAACCAGCACAACGACGCTGTCCTTTACCAAGG
                                 ttctaac  putative branch site (score: 10)
                                           ttgccccc  putative PPT
     tttttttttactaatt  TA-rich tract