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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAGGGCCCCCAGCAAGCTATCATCTGCGTTTTCTGGTACTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaatgatgatctttaagaacttcccaagacctaataacacgaacctgacacactcgtgggaaacattaataacgatcaataatttctcttccccaactaataactagattctaatggcagcgtatgtagtaatgctaacaaaattgttctcttcttcag

Basic information

species Zea mays
transcript GRMZM2G024887_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024887_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g45010.1 (Oryza sativa), 5'ss of exon 4
ACAAGGGCCCCCAGCAAGCTATCATCTGCGTTTTCTGGTACTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtaca-gaaatgatgatctttaagaacttcccaagacctaataacacgaacctgacacactcgtgggaaacattaataacgatcaataatttctcttccccaactaataactagattctaatggcagcgtatgtagtaatgctaacaaaattgttctcttcttcag
 |||||||||| |||||| |||  || ||||||||||| |||||||||||||||||||| |||||||||||||||||||| || || |||||||| |     ||| | ||| |      | |||    | | ||       |||  | |  |||  |||   ||||   | | |    | |||  ||    ||  |   | ||| ||                                                 
GCAAGGGCCCCAAGCAAGATATGTTCAGCGTTTTCTGGAACTCAGGATAAGTGTGCAGCCTGCCAGAAAACAGTGTACCCACTAGAAAAGgtacacgctgcaatgctgtttta------ctcaaa---tgaaaat-----tctgtaagaaacgtcagaaggtttaacc-caacctcccacttccattggagaa--acccattagttt-------------------------------------------------
















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|211391775|gb|FL355251.1|FL355251
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGADAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGATTCCTACCACAA
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAA
EST: gi|211455531|gb|FL349675.1|FL349675
EST:     CTCAGGATAAGTGTGCTGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCCTACCACAAGAGCTGCTTCAAGTGCTCGCA
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCC-TACCACAAGAGCTGCTTCAAGTGCTCGCA
EST: gi|21480972|gb|BQ577655.1|BQ577655
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|211378105|gb|FL329996.1|FL329996
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAAGCTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCA
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAA-CTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCA
EST: gi|32869494|gb|CF009176.1|CF009176
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTGACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCG
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCG
EST: gi|32870818|gb|CF010500.1|CF010500
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTGACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|211331555|gb|FL357939.1|FL357939
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|211007496|gb|FL346568.1|FL346568
EST:     CTCAGGATAAGTGTGCTGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|18661649|gb|BM501509.1|BM501509
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTTGGAAAGGCGAGT
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCT-GGAA-GGCGAGT
EST: gi|21480781|gb|BQ577464.1|BQ577464
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|26455128|gb|CA826711.1|CA826711
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|21330893|gb|BQ486274.1|BQ486274
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|21480794|gb|BQ577477.1|BQ577477
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGAGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|116819068|gb|EC862153.1|EC862153
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTAGCACAAGAGCTGCTTCAAAGTGCTCGCA
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAA-GTGCTCGCA
EST: gi|32868868|gb|CF008550.1|CF008550
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTGACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|21331003|gb|BQ486384.1|BQ486384
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|21330183|gb|BQ485564.1|BQ485564
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|9743144|gb|BE519292.1|BE519292
EST:     CTCAGGATAAGTGTGCTGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|32869353|gb|CF009035.1|CF009035
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTGACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|21330046|gb|BQ485441.1|BQ485441
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|21330759|gb|BQ486140.1|BQ486140
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|32906533|gb|CF011346.1|CF011346
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTGACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|211130928|gb|FL366516.1|FL366516
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAA
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAA
EST: gi|50325577|gb|CO520703.1|CO520703
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
EST: gi|21330096|gb|BQ485477.1|BQ485477
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAG
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAG
EST: gi|78109383|gb|DV527799.1|DV527799
EST:     CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAG                         TTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC
genomic: CTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCAC

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 2 RNA-Seq libraries.


Block sizes: 41 (upstream exon), 9 (downstream exon)
Score: 2

ACAAGGGCCCCCAGCAAGCTATCATCTGCGTTTTCTGGTACTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCACGGGGGCTGCATCCTCACCACCTCCTCCTACGCCGCGCTCAACGGCGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 233

ACAAGGGCCCCCAGCAAGCTATCATCTGCGTTTTCTGGTACTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaat ... tcttcttcagTTAACTCTGGAAGGCGAGTCCTACCACAAGAGCTGCTTCAAGTGCTCGCACGGGGGCTGCATCCTCACCACCTCCTCCTACGCCGCGCTCAACGGCGTTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAAGGGCCCCCAGCAAGCTATCATCTGCGTTTTCTGGTACTCAGGATAAGTGTGCAGCTTGCCAGAAAACAGTGTACCCGCTGGAGAAGgtacagaaatgatgatctttaagaacttcccaagacctaataacacgaacctgacacactcgtgggaaacattaataacgatcaataatttctcttccccaactaataactagattctaatggcagcgtatgtagtaatgctaacaaaattgttctcttcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA