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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaagttttcacaaaaaaataacaaagttatgcattatcgcagtaatcatatttctccattaatcaatgtctaaattcattggattctggatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCCCAGAGACCTTTGACTCAATTGTCCTTGATGAAACCAAAGATGTCCTTGT

Basic information

species Zea mays
transcript GRMZM2G128171_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128171_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 4
-ttcaagttttcacaaaaaaataacaaagtta-tgcattatcgcagtaatcatatttctccatta-atcaatgtctaaattcattggattctggatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCCCAGAGACCTTTGACTCAATTGTCCTTGATGAAACCAAAGATGTCCTTGT
 |   ||||| |||||| |  |     ||||| | |||| | | | | |||   |  |||  ||| | ||   | |||  |||| | ||| |     |||||||||| ||||||||||||||||||||||||||||||||||| || ||   |||||| | ||||||||||||||| |||||||||| ||||||  | |||||
gtcttagtttccacaaacagcttcttgagttaattcatttttgtatttatctcttcactcggttacaacagcatataa--tcat-gaattttcctgatttcagGCACTAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTAGTGCTTGGCCCAGACAACTTTGACTCAATTGTTCTTGATGAAAACAAAGACATTCTTGT
















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|149086778|gb|EE176319.2|EE176319
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|211242630|gb|FL145170.1|FL145170
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|211247092|gb|FL145190.1|FL145190
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGT
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGT
EST: gi|148936842|gb|EC880983.2|EC880983
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|148972619|gb|EE023578.2|EE023578
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|211242621|gb|FL145161.1|FL145161
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTCAAGGAG                         GCACAAATGTAAAGCTGGCAACCATT
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATT
EST: gi|211244855|gb|FL145175.1|FL145175
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCA
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCA
EST: gi|211251556|gb|FL145219.1|FL145219
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTT
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTT
EST: gi|211244856|gb|FL145176.1|FL145176
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGC
EST: gi|211247097|gb|FL145195.1|FL145195
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAA
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAA
EST: gi|71324810|gb|DR799111.1|DR799111
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|31358980|gb|CD443337.1|CD443337
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|211247095|gb|FL145193.1|FL145193
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAAGTGTTGTGGTTCTCACC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAA-GTGTTGTGGTTCTCACC
EST: gi|211251557|gb|FL145220.1|FL145220
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTG
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTG
EST: gi|211242629|gb|FL145169.1|FL145169
EST:     GGACAACGCACTGCAGGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAA
genomic: GGACAACGCACTGCAG-AAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAA
EST: gi|211247096|gb|FL145194.1|FL145194
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|211249329|gb|FL145207.1|FL145207
EST:     AGGACAACGCACTGCAGAAGCCCTTGCNGAATTTCTCAATACTGAAGGAG                         GCCACAAATGTAAAGCTGGC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGC-ACAAATGTAAAGCTGGC
EST: gi|211247100|gb|FL145198.1|FL145198
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACC
EST: gi|78117470|gb|DV535857.1|DV535857
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|211249338|gb|FL145216.1|FL145216
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|211249332|gb|FL145210.1|FL145210
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTG
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTG
EST: gi|211242626|gb|FL145166.1|FL145166
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGC
EST: gi|78118070|gb|DV536457.1|DV536457
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|148932445|gb|EC876161.2|EC876161
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|67015622|gb|CO444371.1|CO444371
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|149081234|gb|EE170345.2|EE170345
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|211249340|gb|FL145218.1|FL145218
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAG
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAG
EST: gi|71309004|gb|DR790767.1|DR790767
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|148959024|gb|EE010535.2|EE010535
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
EST: gi|193502896|gb|AM937546.1|AM937546
EST:     AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAG                         GCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC
genomic: AGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCC

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: 212

GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCCCAGAGACCTTTGACTCAATTGTCCTTGATGAAACCAAAGATGTCCTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 503

GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCCCAGAGACCTTTGACTCAATTGTCCTTGATGAAACCAAAGATGTCCTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 502

GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCCCAGAGACCTTTGACTCAATTGTCCTTGATGAAACCAAAGATGTCCTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 822

GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGgtgggaattt ... gatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCCCAGAGACCTTTGACTCAATTGTCCTTGATGAAACCAAAGATGTCCTTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcatatttctccattaatcaatgtctaaattcattggattctggatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCCCAGAGACCTTTGACTCAATTGTCCTTGATGAAACCAAAGATGTCCTTGT
                        gtctaaa  putative branch site (score: 822)
                                               tttttc  putative PPT
              attaatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaagttttcacaaaaaaataacaaagttatgcattatcgcagtaatcatatttctccattaatcaatgtctaaattcattggattctggatttttcagGCACAAATGTAAAGCTGGCAACCATTCCTTCAAGTGTTGTGGTTCTCACCCCAGAGACCTTTGACTCAATTGTCCTTGATGAAACCAAAGATGTCCTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - -aaaaaaa
- - - - - - - - - - taacaaa
- - - - - - - - - - - - - - - atgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattctg