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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgacaaataccttttggtacagagccagaacaatttttttgacatgtcttgtacttacaatttaacattttctaacaatatcaatgatgtttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG

Basic information

species Zea mays
transcript GRMZM2G059039_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059039_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g20930.1 (Oryza sativa), 3'ss of exon 14
--atgacaaataccttttggtacagagccagaacaatttttttgacatgtcttgtacttacaatttaacattttctaac--aatatcaatgatgtttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG
  | | |||      |    || |  ||  |   | |  |  | | |  |    ||| || |  || |   ||||||||  ||  | |   |||||  |||||| | |||| | | ||||||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || ||| ||||| |||| | | ||||
acacggcaatg--tatgaaatatactgcttgtgta-tactaataatac-taacctacctaaatgtttatgctttctaactaaacgtgatgaatgttcatttcagCCGTTGCGTGCGAAATCCCCTTTATTTATTGGTGACAAGAAAATCACTCTCTCATGGATGGAGCAGCCAAAGAAACCAGCACCTACAACAACAGG

upper sequence: GRMZM2G059039_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv19s0014g01790.t01 (Vitis vinifera), 3'ss of exon 14
atgacaaataccttttggtacagagccagaacaatttttttgacatgtcttgtacttacaatttaacattttctaacaatatcaatgatgtttct--ttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG-----
                            |||   |||| || | ||| ||| |    |   |   |||  |||          ||   ||||  |  | ||| |||||||||||||||| |||| |||||| || ||| ||||||||| | |||||||||   |     | ||     ||||  |  | |  || |      
--------------------------gtgaatggttttctt-atatgcctt-tctaaatggtcacacacattcggttttctctaacattgttcataatccagCCATTGCATTCAAAATCACCTTCATTTATTGGAGATCAGAAAATCAATTTGTCATGGAAAAAAGCAGCAAAGCCTTCAGCCCCCCCAACTGCTGCATCAT
















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|211513339|gb|FL030355.1|FL030355
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGGGATAAGAA
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAA
EST: gi|32844847|gb|CD984528.1|CD984528
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|37398128|gb|CF636373.1|CF636373
EST:     TTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTNATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|9732110|gb|BE510862.1|BE510862
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|26558849|gb|CA831084.1|CA831084
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|87156817|gb|DY401606.1|DY401606
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|29544218|gb|CB604598.1|CB604598
EST:     GCAATGACCCAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: GCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|29544428|gb|CB604808.1|CB604808
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|32844395|gb|CD984076.1|CD984076
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|32844458|gb|CD984139.1|CD984139
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|60352216|gb|DN219189.1|DN219189
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|29544594|gb|CB604974.1|CB604974
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|22546055|gb|BU098376.1|BU098376
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|32843825|gb|CD983506.1|CD983506
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|67024010|gb|CO452759.1|CO452759
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|31357379|gb|CD441736.1|CD441736
EST:     CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: CTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
EST: gi|149105665|gb|EE291221.2|EE291221
EST:     GCAATGACACAG                         TCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG
genomic: GCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTG

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: 204

AAAGGCGATCAGCAAACTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 53

AAAGGCGATCAGCAAACTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

AAAGGCGATCAGCAAACTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

AAAGGCGATCAGCAAACTTCAACAAGGACAATGAGGTCATATAACAATATATTGGCAATGACACAGgtgatttctt ... tttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcttgtacttacaatttaacattttctaacaatatcaatgatgtttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG
                         ttctaac  putative branch site (score: 52)
                                           tgtttctttc  putative PPT
          ttacaatttaacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgacaaataccttttggtacagagccagaacaatttttttgacatgtcttgtacttacaatttaacattttctaacaatatcaatgatgtttctttcagTCATTGCATTCAAAATCCCCTTTATTTATCGGTGATAAGAAAATCACTCTGTCATGGATGGAGCAGCCCAACAAAGCAGCAGCTACGAAAGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - ttttggt
- - - - - - - - - - - - - - gaacaat
- - - - - - - - - - - - - - - - - - - - tgacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgatg