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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgctgcgtgctgcatgcaaattgcgaccttgtaactgttattctcatgctgctcccctgttcttctgtatatgcctatacgcagGGCCTGCCAAGCGTTACGTGACTACCTCCCCATCGCGTTGAGGGACGGGACATTCAACGGCTTAATCGAG

Basic information

species Zea mays
transcript AC191251.3_FGT005
intron # 7
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|148981581|gb|EE027738.2|EE027738
EST:     ACGCTTAAGAACACAATCCGCTGCTACCTCAGGCTGACAGATGATCGAAG                         GGCCTGCCAAGCCGT-ACGTGACTACCTCCCCATCGCGTTGAGGGACGGGA
genomic: ACGCTTAAGAACACAATCCGCTGCTACCTCAGGCTGACAGATGATCGAAGgtttgtgctg ... ctatacgcagGGCCTGCCAAGC-GTTACGTGACTACCTCCCCATCGCGTTGAGGGACGGGA
EST: gi|71757155|gb|DR955092.1|DR955092
EST:     ACGCTTAAGAACACAATCCGCTGCTACCTCAGGCTGACAGATGATCGAAG                         GGCCTGCCAAGCGTTACGTGACTACCTCCCCATCGCGTTGAGGGACGGGAC
genomic: ACGCTTAAGAACACAATCCGCTGCTACCTCAGGCTGACAGATGATCGAAGgtttgtgctg ... ctatacgcagGGCCTGCCAAGCGTTACGTGACTACCTCCCCATCGCGTTGAGGGACGGGAC
EST: gi|93014334|gb|EB639854.1|EB639854
EST:     ACGCTTAAGAACACAATCCGCTGCTACCTCAGGCTGACAGATGATCGAAG                         GGCCTGCCAAGCGTTACGTGACTACCTCCCCATCGCGTTGAGGGACGGGAC
genomic: ACGCTTAAGAACACAATCCGCTGCTACCTCAGGCTGACAGATGATCGAAGgtttgtgctg ... ctatacgcagGGCCTGCCAAGCGTTACGTGACTACCTCCCCATCGCGTTGAGGGACGGGAC

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), 47 (downstream exon)
Score: 23

ATGTGCTAGCTCAGATGGTCGAAGCACTTGCTGAACAGCCTTCCCCGAGGACGCTTAAGAACACAATCCGCTGCTACCTCAGGCTGACAGATGATCGAAGgtttgtgctg ... ctatacgcagGGCCTGCCAAGCGTTACGTGACTACCTCCCCATCGCGTTGAGGGACGGGACATTCAACGGCTTAATCGAG


Block sizes: 32 (upstream exon), 45 (downstream exon)
Score: 4

ATGTGCTAGCTCAGATGGTCGAAGCACTTGCTGAACAGCCTTCCCCGAGGACGCTTAAGAACACAATCCGCTGCTACCTCAGGCTGACAGATGATCGAAGgtttgtgctg ... ctatacgcagGGCCTGCCAAGCGTTACGTGACTACCTCCCCATCGCGTTGAGGGACGGGACATTCAACGGCTTAATCGAG


Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 5

ATGTGCTAGCTCAGATGGTCGAAGCACTTGCTGAACAGCCTTCCCCGAGGACGCTTAAGAACACAATCCGCTGCTACCTCAGGCTGACAGATGATCGAAGgtttgtgctg ... ctatacgcagGGCCTGCCAAGCGTTACGTGACTACCTCCCCATCGCGTTGAGGGACGGGACATTCAACGGCTTAATCGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 21

ATGTGCTAGCTCAGATGGTCGAAGCACTTGCTGAACAGCCTTCCCCGAGGACGCTTAAGAACACAATCCGCTGCTACCTCAGGCTGACAGATGATCGAAGgtttgtgctg ... ctatacgcagGGCCTGCCAAGCGTTACGTGACTACCTCCCCATCGCGTTGAGGGACGGGACATTCAACGGCTTAATCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaactgttattctcatgctgctcccctgttcttctgtatatgcctatacgcagGGCCTGCCAAGCGTTACGTGACTACCTCCCCATCGCGTTGAGGGACGGGACATTCAACGGCTTAATCGAG
 ttgtaac  putative branch site (score: 21)
 tgttatt  TA-rich tract