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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagagggagaatcagcatccgagagaaaggcaaacagcaaaaaacatgatatgaacttttttttatgtttcactgatcactgatgtcgtcgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA

Basic information

species Zea mays
transcript GRMZM2G080375_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080375_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 1
tcagagggagaatcagcatccgagagaaaggcaaacagcaa-------aaaacatgatatgaacttttttttatgtttca-ctgatcac----tgatgtcgtcgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
            |||   || | | |  | ||    |   |         |  ||  | |  ||    |||  ||   || ||| ||||    |  ||| |  ||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||
------------tcaatttctgtgggcgatgcgcctactgattgagctgcagtatcgttttgaccccatttcttgaagcaactgctcacctgctactgttgctgatctgcagACTTACCCGAATCCTCTGCAAGACAACCCGGCTTATTCAGTCGTCAA

upper sequence: GRMZM2G080375_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 1
-tcagagggagaatcagcatccgagagaaaggcaaacagcaaaaaacatgatatg-aacttttttttatgtttcactgatcactgatgtcgtcgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
    |  | || |  | |||  ||  || |    |    ||     | |    || ||  ||  || |||| | | |  |   |  ||  ||    |||||||||||||| |||||| | ||||||||||| || |||||||| || ||
acatgcagtaggaaaaacata-gatggataatgtattgccattttcctttgagtgcaagattaattaatgtctgattt-tatgtattggtgtgttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA

upper sequence: GRMZM2G080375_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 1
tcagagggagaatcagcatccgagagaaaggcaaac--agcaaaaaacatgatatgaacttttttttatgtttcactgatcactgatgtcgtcgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
  |   |||| |  | |||    ||  || | |     |          ||     ||  ||  || |||| | | |  |   || ||  ||    |||||||||||||| |||||| | ||||||||||| || |||||||| || ||
-taagaggaggaaaaacatagatgaataatgtatctttaatttttcctttgggtacaagattaattaatgtctgattt-tatgtgttggtgtgttgctgcagACATACCCTAATCCTTTGCAAGACAACCCTGCTTATTCAGTTGTTAA

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|74234373|gb|DT642287.1|DT642287
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|211522284|gb|FL320492.1|FL320492
EST:     ACGTGCTCGAGGACGTACCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|148940563|gb|EC885365.2|EC885365
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|211143668|gb|FL321938.1|FL321938
EST:     ACGTGCTCGAGGACGTACCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|149076118|gb|EE164702.2|EE164702
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|148941151|gb|EC886025.2|EC886025
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|18661967|gb|BM501673.1|BM501673
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|76914829|gb|DV165709.1|DV165709
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|37416938|gb|CF646120.1|CF646120
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|149087521|gb|EE176918.2|EE176918
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|76290797|gb|DV030365.1|DV030365
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|149069151|gb|EE157880.2|EE157880
EST:     ACCTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGGCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|149111238|gb|EE294735.2|EE294735
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|76913985|gb|DV165359.1|DV165359
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|78078027|gb|DV506442.1|DV506442
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
EST: gi|148935767|gb|EC879810.2|EC879810
EST:     ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCG                         ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
genomic: ACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA

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), 22 (downstream exon)
Score: 14

GGCGAGTAAGTGGGCGACGAAGAAGAAGCTGGTGGGCGGCGACGCCGGCTACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

GGCGAGTAAGTGGGCGACGAAGAAGAAGCTGGTGGGCGGCGACGCCGGCTACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 272

GGCGAGTAAGTGGGCGACGAAGAAGAAGCTGGTGGGCGGCGACGCCGGCTACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 57

GGCGAGTAAGTGGGCGACGAAGAAGAAGCTGGTGGGCGGCGACGCCGGCTACGTGCTCGAGGACGTGCCGCACCTCACGGATTACATGCCCCAGCTCCCGgtgcgttcga ... cgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgatatgaacttttttttatgtttcactgatcactgatgtcgtcgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA
                                 cactgat  putative branch site (score: 57)
     tatgaactttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagagggagaatcagcatccgagagaaaggcaaacagcaaaaaacatgatatgaacttttttttatgtttcactgatcactgatgtcgtcgatctgcagACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA

- - - - - - -cagcatc
- - - - - - - - - - -gagagaaa
- - - - - - - - - - - - - - - gcaaaca
- - - - - - - - - - - - - - - - - - - caaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgt