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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcacggcgcccacattgcatgtctgttgattccgtcttctgctttggtcaaatccatcttacccttccaagcaatatttttctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGCTGCTGATGAAGCTAAGACAGGCCTCCACAAACTTTCAAAG

Basic information

species Zea mays
transcript GRMZM2G155437_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g01420.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------gcacggcgcccacattgcatgtctgt-tgattccgtcttctgctttgg-tcaaatccatcttacccttccaagcaatatttttctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGCTGCTGATGAAGCTAAGACAGGCCTCCACAAACTTTCAAAG
                                                                                                      |   ||  | |||    || |   | |  || |     ||  | | | |    |   |  |    |||  | ||   |   | | |  ||||||||| || ||||| |||||||| |||||||||||||||||||||||| |||||||||||||||| |||||||| || |||||||| |||
gtagctgcctcttattattattagtctagccagtacggtgcctctctgctcaaagcatcaaacgatatgctgcatagattgaattttggcttttcgctttaaccttgcaactacaacatatttgcatgtatttgcaaaagctattctagattggctgtttgatgaaattctta-catactccctttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGCTGGGGCGTTCATCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAG

upper sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g01430.1 (Oryza sativa), 3'ss of exon 2
---------gcacggcgcccacattgcatgtctgttgattc-cgtcttctgcttt-ggtcaaatccatcttacccttccaagcaatatttttctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGCTGCTGATGAAGCTAAGACAGGCCTCCACAAACTTTCAAAG
          |   ||  | |||    || |   |  |||  |     ||  | | |||    |   |  |    |||  | ||   |   | | |  ||||||||| || ||||| |||||||| |||||||||||| ||||||||||| |||||||||||||||| |||||||| || |||||||| |||
ttcgctttaaccttgcaactacaacatatttgcatgtatttgcaaaggctattctaggttggctgtttgatgaaattctta-catactccctttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAG
















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|18648715|gb|BM497534.1|BM497534
EST:     GGAATCAGAAGCTCAAGGACCTCAGGGAGCCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: GGAATCAGAAGCTCAAGGACCTCAGGGAG-CAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|211011964|gb|FL302300.1|FL302300
EST:     GGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCGAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: GGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTC-AAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|18450755|gb|BM429033.1|BM429033
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|211011963|gb|FL302299.1|FL302299
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|211520197|gb|FL010166.1|FL010166
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|211520200|gb|FL010169.1|FL010169
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|32907095|gb|CF011908.1|CF011908
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|211011965|gb|FL302301.1|FL302301
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|15100390|gb|BI396181.1|BI396181
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|32838220|gb|CD977898.1|CD977898
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|211011962|gb|FL302298.1|FL302298
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCMGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCA
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCA
EST: gi|211520196|gb|FL010165.1|FL010165
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|211009194|gb|FL302295.1|FL302295
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|211520199|gb|FL010168.1|FL010168
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|211520198|gb|FL010167.1|FL010167
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|78081476|gb|DV509888.1|DV509888
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC
EST: gi|211011966|gb|FL302302.1|FL302302
EST:     AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAG                         GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGC

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: 200

ATGCCGTGGACAAGTACAGCAGCGCCTATGTTTTTACCTACGATAACATGAGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGCTGCTGATGAAGCTAAGACAGGCCTCCACAAACTTTCAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

ATGCCGTGGACAAGTACAGCAGCGCCTATGTTTTTACCTACGATAACATGAGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGCTGCTGATGAAGCTAAGACAGGCCTCCACAAACTTTCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

ATGCCGTGGACAAGTACAGCAGCGCCTATGTTTTTACCTACGATAACATGAGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGCTGCTGATGAAGCTAAGACAGGCCTCCACAAACTTTCAAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 119

ATGCCGTGGACAAGTACAGCAGCGCCTATGTTTTTACCTACGATAACATGAGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcc ... tctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGCTGCTGATGAAGCTAAGACAGGCCTCCACAAACTTTCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgctttggtcaaatccatcttacccttccaagcaatatttttctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGCTGCTGATGAAGCTAAGACAGGCCTCCACAAACTTTCAAAG
                    atcttac  putative branch site (score: 119)
                                       tatttttctgttcc  putative PPT
                                     aatatttttctgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacggcgcccacattgcatgtctgttgattccgtcttctgctttggtcaaatccatcttacccttccaagcaatatttttctgttccagGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGCTGCTGATGAAGCTAAGACAGGCCTCCACAAACTTTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC