Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttcatgatggaaggattcatgtttacactgagccaaaagttcttctagggtttattccatgctctacttcatactggcttttatttttctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGGGTGGTACTGTGACTGACGATGCAAGTGATGAATGGCTTGTTCTGGATCA

Basic information

species Zea mays
transcript GRMZM2G025042_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025042_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g31690.2 (Oryza sativa), 3'ss of exon 1
----tgttcatgatggaaggattcatgtttacactgagccaaaagttcttctagggtttattccatgctctacttcatactggcttttatttttctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGGGTGGTACTGTGACTGACGATGCAAGTGATGAATGGCTTGTTCTGGATCA
     |   || |||   |     || | |||| |   | |  | |   | ||      |    ||| | | |      |||   |   |||| || ||| ||||| |||| |||||||||||||||||||||||||||||||| |||||| | ||||| |||||||| || ||||||||||||||||||||||||||||||||
cagcagcatattatgatcgcggctatatatacagttttctattattctctttataaagga----atggtttgcactgagctgatctcatttttgctaaaaacagAGGTAGCCAGGTCTAAAGGAAGGGTTGCACTCACAACAAACATGGTCCTTGGTGGCACTGTGACAGATGATGCAAGTGATGAATGGCTTGTTCTGGATCA
















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|211402882|gb|FL375613.1|FL375613
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|211443951|gb|FL410271.1|FL410271
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|148953492|gb|EE152999.2|EE152999
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|28910260|gb|CB331350.1|CB331350
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|211223495|gb|FL386114.1|FL386114
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|76014839|gb|DT942009.1|DT942009
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|211444194|gb|FL421114.1|FL421114
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|211066457|gb|FL305317.1|FL305317
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|211220755|gb|FL455708.1|FL455708
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|211426123|gb|FL387523.1|FL387523
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|148995059|gb|EE034374.2|EE034374
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|211385110|gb|FL405372.1|FL405372
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|211116996|gb|FL414299.1|FL414299
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AAATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|211149178|gb|FL419649.1|FL419649
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|78121560|gb|DV539944.1|DV539944
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
EST: gi|78117325|gb|DV535712.1|DV535712
EST:     CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCA                         AGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG
genomic: CGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGG

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: 42

TCCCGCGGTGGCCGCCGTCCGCACCTCCGCTGCTGCTCCGGCGGCGGGGGCGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGGGTGGTACTGTGACTGACGATGCAAGTGATGAATGGCTTGTTCTGGATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

TCCCGCGGTGGCCGCCGTCCGCACCTCCGCTGCTGCTCCGGCGGCGGGGGCGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGGGTGGTACTGTGACTGACGATGCAAGTGATGAATGGCTTGTTCTGGATCA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 75

TCCCGCGGTGGCCGCCGTCCGCACCTCCGCTGCTGCTCCGGCGGCGGGGGCGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGGGTGGTACTGTGACTGACGATGCAAGTGATGAATGGCTTGTTCTGGATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

TCCCGCGGTGGCCGCCGTCCGCACCTCCGCTGCTGCTCCGGCGGCGGGGGCGGGGAGCCCGGGCAGCCGCCGCAAGAAGCTGTGCTCGAGGCCATATCCAgtgagtcgtc ... ctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGGGTGGTACTGTGACTGACGATGCAAGTGATGAATGGCTTGTTCTGGATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctagggtttattccatgctctacttcatactggcttttatttttctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGGGTGGTACTGTGACTGACGATGCAAGTGATGAATGGCTTGTTCTGGATCA
                                  cttttatttttct  CT-rich tract
                                   ttttatttttctgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttcatgatggaaggattcatgtttacactgagccaaaagttcttctagggtttattccatgctctacttcatactggcttttatttttctgaaaccagAGATAGCAAGGTCTAAAGGAAGGGTTGCACTCACAACAAATATGGTCATGGGTGGTACTGTGACTGACGATGCAAGTGATGAATGGCTTGTTCTGGATCA

-gttcatg
- - - - - - - - attcatg
- - - - - - - - - - - - -tacactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catactg