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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGGGCAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctcctgatatgatcatgctattgtagggttgttgcctagttgaggatctataggagatgcaaagctttatctcaagaacaactagttagtcag...

Basic information

species Zea mays
transcript GRMZM2G038588_T03
intron # 3
splice site 5'
intron type U2

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|211060219|gb|FL171340.1|FL171340
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
EST: gi|50338324|gb|CO533450.1|CO533450
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
EST: gi|50338770|gb|CO533896.1|CO533896
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
EST: gi|211060214|gb|FL171335.1|FL171335
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATT
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATT
EST: gi|91870592|gb|EB400974.1|EB400974
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGGAAAAGTACTCTC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
EST: gi|149089655|gb|EE178910.2|EE178910
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
EST: gi|31611805|gb|CD568427.1|CD568427
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
EST: gi|78122374|gb|DV540758.1|DV540758
EST:     CAGGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
EST: gi|93014407|gb|EB639927.1|EB639927
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGC
EST: gi|211063178|gb|FL171360.1|FL171360
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAA-TACTCTC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
EST: gi|211060216|gb|FL171337.1|FL171337
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
EST: gi|211063168|gb|FL171350.1|FL171350
EST:     CAAGGGCGAGAACAGCCGCAGCTCAAGAGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAAGGACTCT
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAA-GTACTCT
EST: gi|211063169|gb|FL171351.1|FL171351
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGNGCCAACAGATTCTGGGAAAAGTACTCTC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
EST: gi|148972546|gb|EE023508.2|EE023508
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTTCT
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACT-CT
EST: gi|71435658|gb|DR816708.1|DR816708
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
EST: gi|71323425|gb|DR798363.1|DR798363
EST:     CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAG                         GGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC
genomic: CAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTC

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: 170

TCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGGGCAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTCTGCAAAATGCTTCTTAGCTGGGCTGCCAAACTGGGCTGGAAGCCTACGT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 67

TCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGGGCAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTCTGCAAAATGCTTCTTAGCTGGGCTGCCAAACTGGGCTGGAAGCCTACGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

TCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGGGCAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTCTGCAAAATGCTTCTTAGCTGGGCTGCCAAACTGGGCTGGAAGCCTACGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 43

TCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGGGCAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctc ... tctggcttagGGACCTAGAGTGATTGTTGTGGGGCCAACAGATTCTGGAAAAAGTACTCTCTGCAAAATGCTTCTTAGCTGGGCTGCCAAACTGGGCTGGAAGCCTACGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAATGGTAATTTATGTCAACACGCACGCCATTCTGGATGCCCGCAGGGCAAGGGCGAGAACAGCCGCAGCTCAGGGGGGCGATAAGGAGGCATCACAGgtgagtgctcctgatatgatcatgctattgtagggttgttgcctagttgaggatctataggagatgcaaagctttatctcaagaacaactagttagtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG