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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttctgtttgtctctccttgcatgattttttaaatattctctattctgaaatatattgtggctgtgtcactaaacattgatttttactcattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAGATTAAAAACGTCATTATAGCCAGTGCCACCCGGAAAAGAGAACGCTCGG

Basic information

species Zea mays
transcript GRMZM5G887631_T01
intron # 11
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|211275150|gb|FL390053.1|FL390053
EST:     AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAG                         CTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAG
genomic: AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAG
EST: gi|32937524|gb|CF042343.1|CF042343
EST:     AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAG                         CTTTCGGGTCTTTTGCTCGATGAAGCCCAAGT
genomic: AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGT
EST: gi|32937521|gb|CF042340.1|CF042340
EST:     AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAG                         CTTTCGGGTCTTTTGCTCGATGAAGCCCAAGT
genomic: AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGT
EST: gi|32833306|gb|CD972984.1|CD972984
EST:     AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAG                         CCTTTCGGGTCTTTTGCTCGATGAAGCCCAAGT
genomic: AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagC-TTTCGGGTCTTTTGCTTGATGAAGCCCAAGT
EST: gi|32935366|gb|CF040178.1|CF040178
EST:     AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAG                         CTTTCGGGTCTTTTGCTCGATGAAGCCCAAGT
genomic: AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGT
EST: gi|211217762|gb|FL412345.1|FL412345
EST:     AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAG                         CTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAG
genomic: AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAG
EST: gi|32935549|gb|CF040361.1|CF040361
EST:     AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAG                         CCTTTCGGGTCTTTTGCTCGATGAAGCCCAAGTA
genomic: AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagC-TTTCGGGTCTTTTGCTTGATGAAGCCCAAGTA
EST: gi|32850147|gb|CD989828.1|CD989828
EST:     AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAG                         CCTTTCGGGTCTTTTGCTCGATGAAGCCCAAGT
genomic: AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagC-TTTCGGGTCTTTTGCTTGATGAAGCCCAAGT
EST: gi|32937789|gb|CF042608.1|CF042608
EST:     AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAG                         CTTTCGGGTCTTTTGCTCGATGAAGCCCAAGTA
genomic: AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTA
EST: gi|211325392|gb|FL371045.1|FL371045
EST:     AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAG                         CTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAG
genomic: AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAG
EST: gi|32850586|gb|CD990267.1|CD990267
EST:     AAACAGAAATGTGCTCATCCATGCTGGATCCTTTAAACGAGTGTATGCAG                         CTTTCGGGTCTTTTGCTCGATGAAGCCCAAGT
genomic: AAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGT

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), 44 (downstream exon)
Score: 101

GAGCCAGAAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAGATTAAAAACGTCATTATAGCCAGTGCCACCCGGAAAAGAGAACGCTCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

GAGCCAGAAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAGATTAAAAACGTCATTATAGCCAGTGCCACCCGGAAAAGAGAACGCTCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

GAGCCAGAAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAGATTAAAAACGTCATTATAGCCAGTGCCACCCGGAAAAGAGAACGCTCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

GAGCCAGAAACAGAAATGTGCTCATCCATGCTGGATTCTTTAAACGAGTGTATGCAGgtgtgtaaca ... cattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAGATTAAAAACGTCATTATAGCCAGTGCCACCCGGAAAAGAGAACGCTCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgaaatatattgtggctgtgtcactaaacattgatttttactcattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAGATTAAAAACGTCATTATAGCCAGTGCCACCCGGAAAAGAGAACGCTCGG
                                     tttttactc  CT-rich tract
                           taaacattgattttta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagttctgtttgtctctccttgcatgattttttaaatattctctattctgaaatatattgtggctgtgtcactaaacattgatttttactcattgaacagCTTTCGGGTCTTTTGCTTGATGAAGCCCAAGTACGAGCTATCATAGATGAGATTAAAAACGTCATTATAGCCAGTGCCACCCGGAAAAGAGAACGCTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - tgtttgt
- - - - - - - - - - tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaaaca