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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCATTGTTTGAAGAATGTGGGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcatatccttctattttatgttgcttgtatgtggtggttgttggggacctttgaaggtgatgtctgaataattatgttttgtgcttgttcatgtcaattttgtctgctag

Basic information

species Zea mays
transcript GRMZM2G047093_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047093_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g43030.2 (Oryza sativa), 5'ss of exon 7
ATATCATTGTTTGAAGAATGTGGGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcatatccttctattttatgttgcttgtatgtggtggttgttggggacctttgaaggtgatgtctgaataattatgttttgtgcttgttcatgtcaattttgtctgctag
|| |||||||| || |||||||||||||| |||||||| |||||||| |||||||||||||||||||||||||| |||| |||| ||||   | ||||       |   |     | ||      ||  ||| |    |     |||||||| ||||     |                        
ATTTCATTGTTCGAGGAATGTGGGATGCTGGACAGAGCTCTTGAGGAGATGCAGAAGAAGGAGAGCAAAATTgtaagtcttatctttctcaatcatgtaa-----agaggaaaaatatta-----ctcagaaagatgggcgcacataattatttttttcttctag----------------------

upper sequence: GRMZM2G047093_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g07180.1 (Oryza sativa), 5'ss of exon 2
ATATCATTGTTTGAAGAATGTGGGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcatatccttctattttatgttgcttgtatgtggtggttgttggggacctttgaaggtgatgtctgaataattatgttttgtgcttgttcatgtcaattttgtctgctag
|| |||||||| || |||||    ||||| |||||||| |||||||| |||||||| ||||| ||||||||||| |||| |||| || |   | ||||       | | ||    | ||      ||  ||  |    |     |||||||| |||| | || |                       
ATTTCATTGTTCGAGGAATGCATAATGCTGGACAGAGCTCTTGAGGAGATGCAGAAAAAGGATAGCAAAATTgtaagtcttatctttttcaatcatgta------aagaggaaaatatta-----ctcagacagatgggcgcacataattatttttttttctag-----------------------
















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|22490182|gb|BU050105.1|BU050105
EST:     GAAATGCAGAAGAAGGAGAGCAAAATT                         GTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
genomic: GAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
EST: gi|32930286|gb|CF035098.1|CF035098
EST:     GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATT                         GTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
genomic: GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
EST: gi|31349081|gb|CD433438.1|CD433438
EST:     GGATGCTAGACAGAGCCCCTGAAGAAATGCAGAAGAAGGAGAGCAAAATT                         GTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTCGTTCAAACTT
genomic: GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
EST: gi|18654934|gb|BM499739.1|BM499739
EST:     GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATT                         GTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGNCTTGTTCAAACTT
genomic: GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
EST: gi|76013182|gb|DT940352.1|DT940352
EST:     GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATT                         GTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGGTCAAACTT
genomic: GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
EST: gi|18963330|gb|BM660374.1|BM660374
EST:     GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATT                         GTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
genomic: GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
EST: gi|32933101|gb|CF037913.1|CF037913
EST:     GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATT                         GTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
genomic: GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
EST: gi|32943122|gb|CF047941.1|CF047941
EST:     GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATT                         GTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
genomic: GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
EST: gi|18661955|gb|BM501667.1|BM501667
EST:     GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATT                         GTTGACAAGCTATCATTCAAAGAACAAATGGCATCC
genomic: GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCC
EST: gi|33095320|gb|CF055314.1|CF055314
EST:     GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATT                         GTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT
genomic: GGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 208

ATATCATTGTTTGAAGAATGTGGGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTTGGCCGCTTTGATGAATCTGAGAGCATATACAGATCCCTGCTTTTTATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170

ATATCATTGTTTGAAGAATGTGGGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTTGGCCGCTTTGATGAATCTGAGAGCATATACAGATCCCTGCTTTTTATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

ATATCATTGTTTGAAGAATGTGGGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTTGGCCGCTTTGATGAATCTGAGAGCATATACAGATCCCTGCTTTTTATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

ATATCATTGTTTGAAGAATGTGGGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcata ... tgtctgctagGTTGACAAGCTATCATTCAAAGAACAAATGGCATCCGTCTTGTTCAAACTTGGCCGCTTTGATGAATCTGAGAGCATATACAGATCCCTGCTTTTTATGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATCATTGTTTGAAGAATGTGGGATGCTAGACAGAGCCCTTGAGGAAATGCAGAAGAAGGAGAGCAAAATTgtgagtcatatccttctattttatgttgcttgtatgtggtggttgttggggacctttgaaggtgatgtctgaataattatgttttgtgcttgttcatgtcaattttgtctgctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA