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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatatctggcccatttttttattgaatctgtgcattcttctccttttattgtaaagaattttctaacttttctcattaccagACAACAACCAAGAAAAAGATTTCTTCGTCTTTCAGTTTCCCAGGGCAGCTTGATATGGGAAAACGGTTGTCAAACCCTACATCTAGTTATACATATGAAC

Basic information

species Zea mays
transcript GRMZM2G376074_T02
intron # 4
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|32932408|gb|CF037220.1|CF037220
EST:     TTCCTCCAGTTGTTAATTTTCAGCTGAAGCGTTATGTATTCCTTCCGAAG                         ACAACAACCAAGAAAAAGATTTCTTCGTCTTTCAGTTTCCCAGGGCAGCTT
genomic: TTCCTCCAGTTGTTAATTTTCAGCTGAAGCGTTATGTATTCCTCCCGAAGgtgatatctg ... tcattaccagACAACAACCAAGAAAAAGATTTCTTCGTCTTTCAGTTTCCCAGGGCAGCTT
EST: gi|32933527|gb|CF038339.1|CF038339
EST:     TTCCTCCAGTTGTTAATTTTCAGCTGAAGCGTTATGTATTCCTTCCGAAG                         ACAACAACCAAGAAAAAGATTTCTTCGTCTTTCAGTTTCCCAGGGCAGCTT
genomic: TTCCTCCAGTTGTTAATTTTCAGCTGAAGCGTTATGTATTCCTCCCGAAGgtgatatctg ... tcattaccagACAACAACCAAGAAAAAGATTTCTTCGTCTTTCAGTTTCCCAGGGCAGCTT

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: 234

ATCATGTCAGAAAAGGGTAGACGCCACTCGCTGCATAAAACTTAGATCACTTCCTCCAGTTGTTAATTTTCAGCTGAAGCGTTATGTATTCCTCCCGAAGgtgatatctg ... tcattaccagACAACAACCAAGAAAAAGATTTCTTCGTCTTTCAGTTTCCCAGGGCAGCTTGATATGGGAAAACGGTTGTCAAACCCTACATCTAGTTATACATATGAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 60

ATCATGTCAGAAAAGGGTAGACGCCACTCGCTGCATAAAACTTAGATCACTTCCTCCAGTTGTTAATTTTCAGCTGAAGCGTTATGTATTCCTCCCGAAGgtgatatctg ... tcattaccagACAACAACCAAGAAAAAGATTTCTTCGTCTTTCAGTTTCCCAGGGCAGCTTGATATGGGAAAACGGTTGTCAAACCCTACATCTAGTTATACATATGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

ATCATGTCAGAAAAGGGTAGACGCCACTCGCTGCATAAAACTTAGATCACTTCCTCCAGTTGTTAATTTTCAGCTGAAGCGTTATGTATTCCTCCCGAAGgtgatatctg ... tcattaccagACAACAACCAAGAAAAAGATTTCTTCGTCTTTCAGTTTCCCAGGGCAGCTTGATATGGGAAAACGGTTGTCAAACCCTACATCTAGTTATACATATGAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 118

ATCATGTCAGAAAAGGGTAGACGCCACTCGCTGCATAAAACTTAGATCACTTCCTCCAGTTGTTAATTTTCAGCTGAAGCGTTATGTATTCCTCCCGAAGgtgatatctg ... tcattaccagACAACAACCAAGAAAAAGATTTCTTCGTCTTTCAGTTTCCCAGGGCAGCTTGATATGGGAAAACGGTTGTCAAACCCTACATCTAGTTATACATATGAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgcattcttctccttttattgtaaagaattttctaacttttctcattaccagACAACAACCAAGAAAAAGATTTCTTCGTCTTTCAGTTTCCCAGGGCAGCTTGATATGGGAAAACGGTTGTCAAACCCTACATCTAGTTATACATATGAAC
                                 ttctaac  putative branch site (score: 118)
                               ttttctaacttttctc  CT-rich tract
                ttttattgtaaagaat  TA-rich tract