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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGCATGATTGTTGGAGGATGGGATAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattttgcccataaagttgcattgttcctttctttcaagtagtatttcaatgccacttccattatcctcttggctgtaacatatcttttgtgctct...

Basic information

species Zea mays
transcript GRMZM2G374881_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G374881_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g53060.1 (Oryza sativa), 5'ss of exon 5
GCTGGCATGATTGTTGGAGGATGGGATAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtata-attttgcccataaagttgcattgttcctttctttcaagtagtatttcaatgccacttcc-attatcctcttggctgtaacatatcttttgtgctct
||||||||||||||||| ||||||||||| || |||||||||||||||||||||||||| ||||||||||| ||  ||| ||||||||||||||| ||||||||| || ||      || ||  | |  ||    ||     | |   ||   ||    | |||| |  | | | |  |     | ||| | | | | |   
GCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGAGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATCGGAGgtatatatattatggcaaatgtctcttcattgggctcagagtaatctaatgggaaacatatttcccaccaacatttgtgtctatatataacatatctaca--

upper sequence: GRMZM2G374881_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 5'ss of exon 5
GCTGGCATGATTGTTGGAGGATGGGATAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattttgcccataaagttgcattg---ttcctttctttcaa---gtagtatttcaatgccacttccattatcctcttggctgtaacatatcttttgtgctct
||||||||||||||||| ||||||||||| || ||||| |||||||||||||||||||| ||||||||||| ||  ||| ||||||||||||||||||||||||  ||   ||   ||  ||    ||    || |||| ||       ||||| |  |||   |  |  | | ||| | ||  | ||  |||||| | ||     
GCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGTGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCATTTGCAATTGGAGgtatgtttcccccagaaatattatggtgaatgtcttttcattgggctcatagtaatcaaataagaaatgtagtctccacctgtgtcta-tatatctat-gta----
















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|29544030|gb|CB604410.1|CB604410
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|29544379|gb|CB604759.1|CB604759
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|71320622|gb|DR797046.1|DR797046
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|78543575|gb|DV621073.1|DV621073
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAACAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|16919306|gb|BM074128.1|BM074128
EST:     CGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|37384781|gb|CF629491.1|CF629491
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAACAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|50338298|gb|CO533424.1|CO533424
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|7135787|gb|AW498266.1|AW498266
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAACAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|18180510|gb|BM381720.1|BM381720
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|7216231|gb|AW562353.1|AW562353
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAACAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|78109399|gb|DV527815.1|DV527815
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|37380555|gb|CF627096.1|CF627096
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAACAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|32848451|gb|CD988132.1|CD988132
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|88749443|gb|DY533584.1|DY533584
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|91049302|gb|EB159720.1|EB159720
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|211272372|gb|FK988496.1|FK988496
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|211050109|gb|FL461719.1|FL461719
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|91872633|gb|EB402590.1|EB402590
EST:     TTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|78109398|gb|DV527814.1|DV527814
EST:     TTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|211272369|gb|FK988493.1|FK988493
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGG
EST: gi|37378375|gb|CF625874.1|CF625874
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAACAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|37387307|gb|CF630846.1|CF630846
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAACAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|148967409|gb|EE018635.2|EE018635
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
EST: gi|7216230|gb|AW562352.1|AW562352
EST:     CTCAGTCCCTCTTGGTGGAACGATCTTGAAACAACCATTTGCAATTGGAG                         GCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG
genomic: CTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGG

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), 47 (downstream exon)
Score: 139

GCTGGCATGATTGTTGGAGGATGGGATAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGGGAATGAGCCAGGAAGAGGCAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 124

GCTGGCATGATTGTTGGAGGATGGGATAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGGGAATGAGCCAGGAAGAGGCAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

GCTGGCATGATTGTTGGAGGATGGGATAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGGGAATGAGCCAGGAAGAGGCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GCTGGCATGATTGTTGGAGGATGGGATAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataatttt ... tgaatcgcagGCTCAGGTTCCAGTTATCTTTATGCACTTCTTGATCATGAATGGAAAGAGGGAATGAGCCAGGAAGAGGCAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGCATGATTGTTGGAGGATGGGATAAGTACGAGGGAGGCCAAATTTTCTCAGTCCCTCTTGGTGGAACGATCTTGAAGCAACCATTTGCAATTGGAGgtataattttgcccataaagttgcattgttcctttctttcaagtagtatttcaatgccacttccattatcctcttggctgtaacatatcttttgtgctct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG