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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATAAGACTAGTCAGAACATCCTTCAATTAGCAAAGGATGCGAAAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagttatttcttacttatctaactatctaagctcctacagtttgatcatcgctattttgtatgcctaagtctgttgaagtaatcaattctagtaaacagaaatttgtctatgaatgcttccgtctgtacaagtatattgcaactttagctgtctaggtactcagggtttcttgttgttttattacag

Basic information

species Zea mays
transcript GRMZM2G108087_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108087_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g47440.2 (Oryza sativa), 5'ss of exon 2
GCATAAGACTAGTCAGAACATCCTTCAATTAGCAAAGGATGCGAAAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagttatttcttacttatctaactatctaagctcctacagtttgatcatcgctattttgtatgcctaagtctgttgaagtaatcaattctagtaaacagaaatttgtctatgaatgcttccgtctgtacaagtatattgcaactttagctgtctaggtactcagggtttcttgttgttttattacag
    ||||||||||| ||||| |||||||| |||||||||||||| || ||||||   |  |||||||| |||||||||| | | ||||| ||||| |||||| ||||  |  |||| ||  || |     |  |  ||     | |     ||||    ||   ||| |||||           | | | || |       |  | |||| ||  ||| |    ||    ||  | || ||  ||| ||  |||| | || |||| || |||             
----AAGACTAGTCATAACATTCTTCAATTGGCAAAGGATGCGAAGGAGAAGCTCAGGAGAGCTGCTGAGGCAGACAAGAACGCCGATACTAGTgttagtagtaatttactgtttattta--taccct--ttgttttagcccagtga-----atttgtcttggacaagactgtt-----------tccaactatatgtgtgatcatgtatgcatctttctgctctta-gtttacttagctaccatag-tgattaggaa-tctgggtatcatgtgcag---------

upper sequence: GRMZM2G108087_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g47440.1 (Oryza sativa), 5'ss of exon 2
GCATAAGACTAGTCAGAACATCCTTCAATTAGCAAAGGATGCGAAAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagttatttcttacttatctaactatctaagctcctacagtttgatcatcgctattttgtatgcctaagtctgttgaagtaatcaattctagtaaacagaaatttgtctatgaatgcttccgtctgtacaagtatattgcaactttagctgtctaggtactcagggtttcttgttgttttattacag
||| ||||||||||| ||||| |||||||| |||||||||||||| || ||||||   |  |||||||| |||||||||| | | ||||| ||||| |||||| ||||  |  |||| ||  || |     |  |  ||     | |     ||||    ||   ||| |||||           | | | || |       |  | |||| ||  ||| |    ||    ||  | || ||  ||| ||  |||| | || |||| || |||             
GCAGAAGACTAGTCATAACATTCTTCAATTGGCAAAGGATGCGAAGGAGAAGCTCAGGAGAGCTGCTGAGGCAGACAAGAACGCCGATACTAGTgttagtagtaatttactgtttattta--taccct--ttgttttagcccagtga-----atttgtcttggacaagactgtt-----------tccaactatatgtgtgatcatgtatgcatctttctgctctta-gtttacttagctaccatag-tgattaggaa-tctgggtatcatgtgcag---------
















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|89251975|gb|DY623761.1|DY623761
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|74235067|gb|DT642981.1|DT642981
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|211183486|gb|FL441241.1|FL441241
EST:     AGATAAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AGAT-AAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|211344769|gb|FL217861.1|FL217861
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGAT
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGAT
EST: gi|78082082|gb|DV510494.1|DV510494
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCCCA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|76286077|gb|DV025645.1|DV025645
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|78093274|gb|DV521648.1|DV521648
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|74234506|gb|DT642420.1|DT642420
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|74239521|gb|DT647435.1|DT647435
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|60336907|gb|DN203880.1|DN203880
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|78117098|gb|DV535485.1|DV535485
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|33467876|gb|CF244925.1|CF244925
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|211347160|gb|FL217865.1|FL217865
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAG
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAG
EST: gi|74234352|gb|DT642266.1|DT642266
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|78074309|gb|DV502743.1|DV502743
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|89756275|gb|DY686358.1|DY686358
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
EST: gi|71768040|gb|DR965977.1|DR965977
EST:     AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGT                         GCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA
genomic: AAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACA

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), 48 (downstream exon)
Score: 61

GCATAAGACTAGTCAGAACATCCTTCAATTAGCAAAGGATGCGAAAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 111

GCATAAGACTAGTCAGAACATCCTTCAATTAGCAAAGGATGCGAAAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 123

GCATAAGACTAGTCAGAACATCCTTCAATTAGCAAAGGATGCGAAAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 85

GCATAAGACTAGTCAGAACATCCTTCAATTAGCAAAGGATGCGAAAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagtt ... tttattacagGCAGACAAGAGGATAGCTGATATGAAGCTTGCCAAAGATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATAAGACTAGTCAGAACATCCTTCAATTAGCAAAGGATGCGAAAGATAAGCTCCAAAAGGCTGCTGAAGCAGACAAGAGCACTGATACAAGTgtcagtagttatttcttacttatctaactatctaagctcctacagtttgatcatcgctattttgtatgcctaagtctgttgaagtaatcaattctagtaaacagaaatttgtctatgaatgcttccgtctgtacaagtatattgcaactttagctgtctaggtactcagggtttcttgttgttttattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA