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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtcttggaacaatttctgctttctaccataatttgttgtgttttatttgtggtttctcatgatatgtaagggaattttgtgttttttcccaaggc...

Basic information

species Zea mays
transcript GRMZM2G120857_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 5'ss of exon 8
TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtc--ttggaacaatttctgctttctaccataatttgttgtgtttta----tttgtggtttctcatgatatgtaagggaattttgtgttttttcccaaggc
 ||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| |      |||||||| ||||||  || | | ||||    ||||| |     ||    ||||  |  |  ||||  |  | || || |   ||        
CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttagacatgaacaattcctgcttcatagcttgatttacgatgtttcaacctatttaaatttcctagtacttgtagagtcagtt-gtatcacttgat-----

upper sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA10G06590.2 (Glycine max), 5'ss of exon 5
---------------------------TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtcttggaacaat--ttctgctttctaccataatttgttgtgttttatttgtggt-ttctcatgatatgtaagggaattttgtgttttttcccaaggc
                            ||||| |||||||| || || |||   || || || ||||| |||||||| || |||||||||||||| |||||||| | |   || | |  |||| | || ||   |   |  |     | | | |||  | || |||||  |||| |     ||||  |   ||     |   
TCTGAGAATGTTTTATGTCTTTTGCAGCTGCAACATTGGTGAGGGCGGTATTGCACTTGCTGAGGCTGTACATGGTTCAGCACCTGATATTGCTGGAAAGgtgagctgtgaaaatactcattctaccttatattgtctgtcctaaacctctttgtgtcctgttgtcatggaatgtgaaatttttttaagaggttgtttca---

upper sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA10G06590.1 (Glycine max), 5'ss of exon 6
TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtcttggaacaat--ttctgctttctaccataatttgttgtgttttatttgtggt-ttctcatgatatgtaagggaattttgtgttttttcccaaggc
 ||||| |||||||| || || |||   || || || ||||| |||||||| || |||||||||||||| |||||||| | |   || | |  |||| | || ||   |   |  |     | | | |||  | || |||||  |||| |     ||||  |   ||     |   
CTGCAACATTGGTGAGGGCGGTATTGCACTTGCTGAGGCTGTACATGGTTCAGCACCTGATATTGCTGGAAAGgtgagctgtgaaaatactcattctaccttatattgtctgtcctaaacctctttgtgtcctgttgtcatggaatgtgaaatttttttaagaggttgtttca---

upper sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 5'ss of exon 6
TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtcttggaacaatt-tctgctttctaccataatttgttgtgttttatttgtggtttctcatgat-atgtaagggaattttgtgttttttcccaaggc
 ||||||||||| || || || |||  ||| || ||||| |||||||||||||| || ||||||||||| ||||| ||    |  | | | | | || ||| |    |  | | |      |   ||||| |    |||    ||| |      ||   |   ||    || |  
CTGCAATATTGGAGAGGGAGGTATTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAGgttagtcactaaagctactgtatgatttttggtctcgtgt-tcactcatgccttgtgttgctacatatccatgcatctatgttcattaacttcattcatgc-

upper sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S83_44V6.1 (Physcomitrella patens), 5'ss of exon 6
TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtcttggaacaatttctgctttctaccataatttgttgtgttttatttgtggtttctcatgatatgtaagggaattttgtgttttttcccaaggc----------
| | || ||||| ||   |||  |     ||   |||||||| |||||  | |||||||||||||||||||||||    |           |   | | || |     | ||  | ||  |  |   ||  || |     ||  | | | |  |   ||  | || ||| | |          
TGGAAACATTGGAGATAATGGATTGGCCTTGATGGAAGCTGTGCATGGAACGGCTCCTGATATTGCTGGCAAGgttgtattcc--------tctcgatctccaatgctagttactctggatcgtccatg--ttatggcagtaaattatgtagctcaatgactatttccacgccaattttttgg

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|37380928|gb|CF627310.1|CF627310
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTT-TGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|76019790|gb|DT946960.1|DT946960
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|211101475|gb|FL457329.1|FL457329
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|110194437|gb|EC876335.1|EC876335
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGTTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|37384660|gb|CF629421.1|CF629421
EST:     GATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: GATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|211216460|gb|FL469131.1|FL469131
EST:     TTT-TCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|31250098|gb|CD219122.1|CD219122
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|74239665|gb|DT647579.1|DT647579
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|44900378|gb|CK826923.1|CK826923
EST:     TGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|23199568|gb|BU582133.1|BU582133
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|87155757|gb|DY400546.1|DY400546
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|5499534|gb|AI855401.1|AI855401
EST:     TTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|29544695|gb|CB605075.1|CB605075
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|32915735|gb|CF020547.1|CF020547
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|33103704|gb|CF063664.1|CF063664
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|16925630|gb|BM078698.1|BM078698
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTGGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|211039065|gb|FL478477.1|FL478477
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|29167895|gb|CB411155.1|CB411155
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|37381420|gb|CF627593.1|CF627593
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|37384800|gb|CF629499.1|CF629499
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|31250137|gb|CD219161.1|CD219161
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
EST: gi|78109385|gb|DV527801.1|DV527801
EST:     TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGC

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: 50

TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGCCACATGCAATTCAACGACAAAGCAGACCGGATCCACAACGCCATCCTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGCCACATGCAATTCAACGACAAAGCAGACCGGATCCACAACGCCATCCTCC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 77

TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGCCACATGCAATTCAACGACAAAGCAGACCGGATCCACAACGCCATCCTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118

TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtctt ... ttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGCCACATGCAATTCAACGACAAAGCAGACCGGATCCACAACGCCATCCTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCAATATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCATGGTTCTGCTCCTGATATTGCTGGCAAGgtgaggtcttggaacaatttctgctttctaccataatttgttgtgttttatttgtggtttctcatgatatgtaagggaattttgtgttttttcccaaggc

- - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - -  GCTGTT