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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcggcattatgttgctcacagctgttgccctttgttgttttgtttatcactaacttgttttctattactag

Basic information

species Zea mays
transcript GRMZM2G145258_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145258_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G04840.1 (Arabidopsis thaliana), 5'ss of exon 4
TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcggcattatgttgctcacagctgttgccctttgttgttttgtttatcact-----aacttgttttctattactag------------------------------
||  || ||||||||||| || || |||||| | ||||||||||| ||| | ||| | ||||||||||| ||||||||||| || ||     | || ||||||| ||| |    | |||||   |||    ||  | |  ||  || || | ||   |     |||     || |  |  | |                              
TTCTCTTGCTGATCTTCAAGGTGATGAGGATAACGCTTACAGGAAGATCCGTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag----tttgttgtaaacattgatttacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttag

upper sequence: GRMZM2G145258_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv05s0020g03900.t01 (Vitis vinifera), 5'ss of exon 4
TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcggcattatgttgctcac--agctgttgccctttgttgttttgt--ttatcactaacttgttttctattactag---------------------------------------------
 |  || ||||| |||||||  || |||||||| ||||| || || ||  | ||  | ||||||||||| || || |||||||| || ||||||||||||||| |||  |  ||  ||  |  |    |  | |    || |||  | || |  ||||   ||  ||  ||| | |   ||                                              
ATCACTTGCTGACCTTCAGGCTGATGAGGATCAGGCTTATAGAAAGATTCGACTGAGAGCTGAAGATGTTCAAGGGAGGAATGTTCTGACAAACTTTTGGgta-tgacagagatcctgaggtcctataaattttcattctatgtaatcttatgattatttttatttttatttatgtatttatttattttttaacaaaatgtttttcttttccttttggaaaatacag

upper sequence: GRMZM2G145258_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0030g01810.t01 (Vitis vinifera), 5'ss of exon 4
TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcggcattatgttgctcacagctgttgccctttgttgttttgtttatcactaacttgttttctattactag---------------
|| ||| ||||||||||||  ||| |||||||| || |||||||| ||| | ||  | ||||| |||||||| || | |||||| ||||||||||| |||||    || |     |||    | |    | ||    ||  ||   |     |     || |||   | | | | |                 
TTCCCTGGCTGATCTTCAGAACGATGAGGATCATGCCTACAGGAAGATCCGACTGAGAGCTGAGGATGTGCAAGGAAAGAATGTCCTCACAAACTTCTGGgtgggcatag----catgacagttagcctttttttttttaattacatgcaaaagaggaaaattggggtttctcattttttttaataatttcag

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|211215691|gb|FL434867.1|FL434867
EST:     GCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCAC-AACTTTTTGG                         GGCATGGATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCA
genomic: GCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAAC-TTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCA
EST: gi|211223878|gb|FL178492.1|FL178492
EST:     GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGG                         GGCATGAATTTTAACCACTGNTAAACTCCAGATCCCTAGTGAAGAAGTGGC
genomic: GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTA-CCACTGATAAACTC-AGATCCCTAGTGAAGAAGTGGC
EST: gi|31360389|gb|CD444746.1|CD444746
EST:     GGCTCCGTGCT-AAGATGTGCAGGGCAGGAATGTGCTCAC-AACTTTTGG                         GGCATGAA-TTTACCCACTGATAAACTCAGATCCCTAGT-AAGAAGTGGCA
genomic: GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTA-CCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCA
EST: gi|84977073|gb|DW475495.1|DW475495
EST:     GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGG                         GGCATGAATTTTACCACCGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
genomic: GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
EST: gi|18384904|gb|BM418103.1|BM418103
EST:     GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGG                         GGTATGAATTTTACCACTGATAAACTCAGATCCCTAGTAAAGAAGTGGCAG
genomic: GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
EST: gi|5005674|gb|AI711736.1|AI711736
EST:     TGCTGAAGATGTGCAGGGCAGGAATGTGCTCCCAAACTTTTGG                         GGCATGGATTTTACCNCTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
genomic: TGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
EST: gi|31357009|gb|CD441366.1|CD441366
EST:     GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGG                         GGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
genomic: GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
EST: gi|83279071|gb|DV943079.1|DV943079
EST:     GCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGG                         GGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
genomic: GCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
EST: gi|67018238|gb|CO446987.1|CO446987
EST:     GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGG                         GGCATGGATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
genomic: GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
EST: gi|213183157|gb|FM184569.1|FM184569
EST:     GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGG                         GGCATGGATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
genomic: GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
EST: gi|67042647|gb|CO468902.1|CO468902
EST:     GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGG                         GGCATGGATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
genomic: GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
EST: gi|67013865|gb|CO442614.1|CO442614
EST:     GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGG                         GGCATGGATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
genomic: GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
EST: gi|84977492|gb|DW475914.1|DW475914
EST:     GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGG                         GGCATGAATTTTACCACCGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
genomic: GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
EST: gi|211234191|gb|FL178563.1|FL178563
EST:     GGCTCCGTGCTGAAGATGTGCAGGGCANGAATGTGCTCACAAACTTTTGG                         GGCATGGATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG
genomic: GGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAG

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: 852

TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAGACATTAATCGAAGCCCATGTTGATGTCAAGACAACCGACAACTACATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 701

TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAGACATTAATCGAAGCCCATGTTGATGTCAAGACAACCGACAACTACATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 546

TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAGACATTAATCGAAGCCCATGTTGATGTCAAGACAACCGACAACTACATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 521

TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcg ... ctattactagGGCATGAATTTTACCACTGATAAACTCAGATCCCTAGTGAAGAAGTGGCAGACATTAATCGAAGCCCATGTTGATGTCAAGACAACCGACAACTACATGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTGAAGATGTGCAGGGCAGGAATGTGCTCACAAACTTTTGGgtaatgatcggcattatgttgctcacagctgttgccctttgttgttttgtttatcactaacttgttttctattactag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG