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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaatgctattccaagtgaacaatgactcatacaccacctttgcagtcgtattaaagctataacacaagtaaccaaccctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATTAATCAACACTTCCATCTTTGTGCCCGATAGGAAATTTTGTGCTTCCCTT

Basic information

species Zea mays
transcript GRMZM2G141587_T02
intron # 25
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|60357952|gb|DN224925.1|DN224925
EST:     TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAG                         GTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATT
genomic: TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAGgtgaaatgct ... cctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATT
EST: gi|32945303|gb|CF050122.1|CF050122
EST:     TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAG                         GTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAGCGGTATT
genomic: TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAGgtgaaatgct ... cctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATT
EST: gi|60359163|gb|DN226136.1|DN226136
EST:     TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAG                         GTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATT
genomic: TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAGgtgaaatgct ... cctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATT
EST: gi|60358722|gb|DN225695.1|DN225695
EST:     TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAG                         GTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATT
genomic: TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAGgtgaaatgct ... cctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATT
EST: gi|32945280|gb|CF050099.1|CF050099
EST:     TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAG                         GTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAGCGGTATT
genomic: TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAGgtgaaatgct ... cctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATT
EST: gi|32943884|gb|CF048703.1|CF048703
EST:     TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAG                         GTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAGCGGTATT
genomic: TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAGgtgaaatgct ... cctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATT
EST: gi|4827713|gb|AI668405.1|AI668405
EST:     TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAG                         GTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAGCGGTATT
genomic: TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAGgtgaaatgct ... cctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATT
EST: gi|12971756|gb|BG267642.1|BG267642
EST:     TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAG                         GTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATT
genomic: TAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAGgtgaaatgct ... cctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATT

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), 47 (downstream exon)
Score: 134

TGCTGACTGAGCAATAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAGgtgaaatgct ... cctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATTAATCAACACTTCCATCTTTGTGCCCGATAGGAAATTTTGTGCTTCCCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

TGCTGACTGAGCAATAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAGgtgaaatgct ... cctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATTAATCAACACTTCCATCTTTGTGCCCGATAGGAAATTTTGTGCTTCCCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 363

TGCTGACTGAGCAATAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAGgtgaaatgct ... cctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATTAATCAACACTTCCATCTTTGTGCCCGATAGGAAATTTTGTGCTTCCCTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 292

TGCTGACTGAGCAATAGTGGATTAACGGATCAGCAACTTCGCTTCAGCGGTGTAGTTTGTAAAGgtgaaatgct ... cctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATTAATCAACACTTCCATCTTTGTGCCCGATAGGAAATTTTGTGCTTCCCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccacctttgcagtcgtattaaagctataacacaagtaaccaaccctattgcagGTTGCTGACTGCTATAGAGTACATGATATCCATTTTTTCCCCAACGGTATTAATCAACACTTCCATCTTTGTGCCCGATAGGAAATTTTGTGCTTCCCTT
                                  aagtaac  putative branch site (score: 292)
                                            ccctatt  putative PPT
                 tattaaagctataa  TA-rich tract