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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttttactgaagtacaacagtgcattttgatttctaaacataagttctaagttgggtcagtttcattttattttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG

Basic information

species Zea mays
transcript GRMZM5G806449_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806449_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g56850.4 (Oryza sativa), 3'ss of exon 6
gtgatttttactgaagtacaacagtgcattttgatttctaaacata--agttctaag------ttgggtcagtttcatttt-attttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG
|||| ||   ||||  | | | |||||||||||||| | |    |     ||  | |      || | || ||||| |||| || | ||||||||||||||||| || || || ||||||||||| ||||| |||||||| ||| |||||||||||||||| || ||||| ||||
gtgagttaagctgacatcctaaagtgcattttgattcccatgtgttctgttttcacgataggttttgatctgtttcttttttatgtaaaccagTTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAG
















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|161407234|gb|DW042290.1|DW042290
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|211287654|gb|FL367858.1|FL367858
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|62550294|gb|DN830714.1|DN830714
EST:     CCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: CCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|8368856|gb|BE051801.1|BE051801
EST:     GGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: GGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|211462691|gb|FL336836.1|FL336836
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|211123447|gb|FL321141.1|FL321141
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|67026810|gb|CO455559.1|CO455559
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|24934176|gb|CA452394.1|CA452394
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGATTAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|211135367|gb|FL349825.1|FL349825
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAN
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|32919439|gb|CF024251.1|CF024251
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|32794339|gb|CD946575.1|CD946575
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|24934507|gb|CA452725.1|CA452725
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|211396212|gb|FL320934.1|FL320934
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|47961736|gb|CN844445.1|CN844445
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|211460047|gb|FL333663.1|FL333663
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|51593048|gb|CV072194.1|CV072194
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|33942527|gb|CF349127.1|CF349127
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|211540781|gb|FL336428.1|FL336428
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|108823920|gb|EC277928.1|EC277928
EST:     GGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: GGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|211318389|gb|FL341246.1|FL341246
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGYAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
EST: gi|24934516|gb|CA452734.1|CA452734
EST:     ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAG                         TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG
genomic: ACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAG

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: 594

AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3336

AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2642

AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 972

AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgattttta ... ttttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgatttctaaacataagttctaagttgggtcagtttcattttattttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG
      ttctaaa  putative branch site (score: 972)
                                   tttcattttatttt  putative PPT
                                 agtttcattttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatttttactgaagtacaacagtgcattttgatttctaaacataagttctaagttgggtcagtttcattttattttaaccagTTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG