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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctatttaaattttgtttgttataatccttttcccattcacattatagaagttgcaacttacaaggtgcagatatttgatgtgtttttggatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACAAATGTGGCGGCTCGTGGTCTGGATATTAATGATGTGCAGCTTATCATTC

Basic information

species Zea mays
transcript GRMZM2G164956_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164956_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os09g34910.1 (Oryza sativa), 3'ss of exon 7
--ctctatttaaatt-ttgtttgttataatccttttcccattcacattatagaagttgcaacttacaaggtgcagatatttgatgtgtttttggatcatt-tagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACAAATGTGGCGGCTCGTGGTCTGGATATTAATGATGTGCAGCTTATCATTC
   | | | | |||  ||  ||  |||  | ||||  | |||   | | |  |    |  |   | ||  || | |||  | |    |   |  ||  || ||||| ||||||||||| ||  | || || |||||    ||||||||||||||||| ||||| || || || ||||| |||||||||||||||||||||||||
tgttatttgtgaataattactttgtatt-ttctttggctatttgtaatgtttagaaggttatcgaaaacatgtatataaatcac---tgaataaatttttgtagGTTATTCTTGCTGGGTTCAGGAGTGGCAAGTTTTTAGTTTTGGTTGCTACAAACGTGGCTGCACGAGGGCTGGACATTAATGATGTGCAGCTTATCATTC

upper sequence: GRMZM2G164956_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G29060.1 (Glycine max), 3'ss of exon 7
----------------------------------------------------------------ctctatttaaattttgtttgttataatccttttcccattcacattatagaagttgcaacttacaaggt-----gcagatatttgatgtgtttttggatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACAAATGTGGCGGCTCGTGGTCTGGATATTAATGATGTGCAGCTTATCATTC
                                                                  ||  |  | |  ||| | || |  | |       |||   |||||||    ||| ||      |||      | |    || ||    |  ||   | |  |||| |  ||  |||| ||| |    ||||| |||  |   || ||||| ||||||||||| ||||| ||||| |||||||||||||| ||| | || || |
gtgagctattacctgaagtttggtttagttattgacttatgaactgttactttaaactttgatatccttatggactgatgtattttgtttttcacaatttattttaattatagtgtgtgccacccttgtggtttcttactgtctcttaattgtgtcctgtcccctgcagGTTACACTGTCTGGCTTTAGGTCTGGGAAATTCATGACATTAGTTGCCACAAATGTGGCAGCTCGAGGTCTTGATATTAATGATGTTCAGTTAATTATAC

upper sequence: GRMZM2G164956_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT5G62190.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------ctctatttaaattttgtttgttataatccttttcccattcacattatagaagttgcaacttacaaggtgcagatatttga---tgtgtttttggatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACAAATGTGGCGGCTCGTGGTCTGGATATTAATGATGTGCAGCTTATCATTC
                                   ||   ||| ||   | |  | |||    |   | |   |  |  |   | |  |||  |  ||   ||| |   | |   || ||  |  ||| ||  |||| | ||||||||||||| | |  || |||||       ||||| ||||||||||| || ||||||||||| ||||| |||||||||||| | || || |
gtatgtgtttaagttttctttcaagctttcttgcataggcaaagttaagtagggagaatttgatcttcttatcctgttaaattgctcaaacagagcagtatcagcttgctaactatgagtcctgtgattat--agGTTACTCTTGCTGGATTTAGGAATGGCAAGTTTGCAACATTGGTGGCTACAAATGTTGCTGCTCGTGGTCTAGATATCAATGATGTGCAGTTAATTATCC

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|22491136|gb|BU051059.1|BU051059
EST:     TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
genomic: TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
EST: gi|32801606|gb|CD953842.1|CD953842
EST:     GATCCACGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
genomic: GATCC-CGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
EST: gi|32798761|gb|CD950997.1|CD950997
EST:     GATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGT
genomic: GATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGT
EST: gi|32789660|gb|CD941896.1|CD941896
EST:     GATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
genomic: GATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
EST: gi|18964493|gb|BM661037.1|BM661037
EST:     TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCA-GCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGC
genomic: TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGC
EST: gi|32928427|gb|CF033239.1|CF033239
EST:     TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
genomic: TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
EST: gi|32846981|gb|CD986662.1|CD986662
EST:     TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
genomic: TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
EST: gi|19272557|gb|BM888813.1|BM888813
EST:     TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
genomic: TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
EST: gi|32929175|gb|CF033987.1|CF033987
EST:     TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
genomic: TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
EST: gi|32801655|gb|CD953891.1|CD953891
EST:     GATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
genomic: GATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
EST: gi|161407373|gb|DW042376.1|DW042376
EST:     TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
genomic: TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
EST: gi|32801868|gb|CD954104.1|CD954104
EST:     CCGTGCCTTGCATGGAGATGTTTTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
genomic: CCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
EST: gi|87153206|gb|DY397995.1|DY397995
EST:     TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
genomic: TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
EST: gi|32795159|gb|CD947395.1|CD947395
EST:     GATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCGGGTTTTGGTTGCTACA
genomic: GATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
EST: gi|32928455|gb|CF033267.1|CF033267
EST:     TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAA                         GTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA
genomic: TTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACA

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: 304

CATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCTTTCTGGTTTGATTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACAAATGTGGCGGCTCGTGGTCTGGATATTAATGATGTGCAGCTTATCATTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 225

CATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCTTTCTGGTTTGATTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACAAATGTGGCGGCTCGTGGTCTGGATATTAATGATGTGCAGCTTATCATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

CATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCTTTCTGGTTTGATTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACAAATGTGGCGGCTCGTGGTCTGGATATTAATGATGTGCAGCTTATCATTC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 90

CATTATCTTCACTGAGACGAAGGATTCTGCATCAGAGCTTTCTGGTTTGATTCCTGGATCCCGTGCCTTGCATGGAGATGTTGTGCAAGCTCAGCGTGAAgtatgtgaat ... gatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACAAATGTGGCGGCTCGTGGTCTGGATATTAATGATGTGCAGCTTATCATTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagaagttgcaacttacaaggtgcagatatttgatgtgtttttggatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACAAATGTGGCGGCTCGTGGTCTGGATATTAATGATGTGCAGCTTATCATTC
                           atatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctatttaaattttgtttgttataatccttttcccattcacattatagaagttgcaacttacaaggtgcagatatttgatgtgtttttggatcatttagGTCATTCTTGCTGGATTTCGTAGCGGGAAGTTCCAGGTTTTGGTTGCTACAAATGTGGCGGCTCGTGGTCTGGATATTAATGATGTGCAGCTTATCATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT