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'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgatcaagcttttattttatatctattcgctgaagtatttattgtctatatctttatcttgccagcgtcttaactttatttctcttgacatctgacctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG

Basic information

species Zea mays
transcript GRMZM2G018508_T01
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018508_T01 (Zea mays), 3'ss of exon 27
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 31
gtacgatcaagcttttattttatatctattcgctgaagtatttattgtctatatctttatcttgccagcgtcttaactttatttctcttgacatctgacctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG
             |  | | | |   |  | ||| ||  | | | |||   |  ||| || | |    | | | |||||| |||  ||||         ||| || || ||||||||||||||||||||||||| |||||||||||||| ||||||||||| |||||||| ||| ||||||    |||||||
------------gtacaatattttcttgcttgctaaa-caatcactgttagtg-cttaatttggttcacatttaaacttt-ttttgcttg---------cttatttagCGAAACATGTATGGAGCTTGGGAGCAATATCTTGGACTGGAGCATCCAGACACGGCTCCTAGAAAGACACACAACGCTAATCAG
















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|4753524|gb|AI657434.1|AI657434
EST:     GACTATTTT-AAGATTCAGATACTGTAGCTTT-AAATTTCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
genomic: GACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
EST: gi|67016472|gb|CO445221.1|CO445221
EST:     GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
genomic: GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
EST: gi|6020900|gb|AW065828.1|AW065828
EST:     GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
genomic: GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
EST: gi|88751977|gb|DY536118.1|DY536118
EST:     GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
genomic: GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
EST: gi|67015347|gb|CO444096.1|CO444096
EST:     GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
genomic: GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
EST: gi|67015345|gb|CO444094.1|CO444094
EST:     GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
genomic: GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
EST: gi|50332269|gb|CO527395.1|CO527395
EST:     GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
genomic: GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
EST: gi|32857251|gb|CD996932.1|CD996932
EST:     GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
genomic: GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
EST: gi|32943477|gb|CF048296.1|CF048296
EST:     GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
genomic: GTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
EST: gi|74238602|gb|DT646516.1|DT646516
EST:     CCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC
genomic: CCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGAC

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: 227

TGGAAGTTTGCATACATTTCACTTGGTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

TGGAAGTTTGCATACATTTCACTTGGTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

TGGAAGTTTGCATACATTTCACTTGGTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

TGGAAGTTTGCATACATTTCACTTGGTCGTCCAGACTATTTTGAAGATTCAGATACTGTAGCTTTAAAATTTCAGgtacgatcaa ... cctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttatcttgccagcgtcttaactttatttctcttgacatctgacctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG
                                             ccttttt  CT-rich tract
                 tcttaactttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgatcaagcttttattttatatctattcgctgaagtatttattgtctatatctttatcttgccagcgtcttaactttatttctcttgacatctgacctttttaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC