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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaacgtttttgcttgagtaccttgtctcctacgtatgtatcgcaatatctcttccactgactggtaggctttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTTGTTAAGCGTGGCATGGAAGTGTTTGTTGCACAATCTTACAGCAAGAACC

Basic information

species Zea mays
transcript GRMZM5G836910_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 3'ss of exon 8
gtgaa-cgtttttgcttgagtaccttgtctcctacgtatgtatcgcaatatctcttccactgactggtaggc-tttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTTGTTAAGCGTGGCATGGAAGTGTTTGTTGCACAATCTTACAGCAAGAACC
|||||  ||| |  ||| | ||  | || |    |   || ||   || |  | |   ||||||| | |    ||||  |  |||||||||||||||||||||||||||||||||||| ||||||||||||||||||| | || ||  |||||||||||||||| || ||||| ||||| ||||
gtgaaatgttctcactttattatttcgtttttctc---tgcatgaaaacaaatatcttactgactagcaaatatttctctgcagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATCTTCTGTCAGGCTTTTTGTTCAACGGGGACTGGAAGTGTTTGTTGCGCAGTCTTATAGCAAAAACC

upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA14G13480.1 (Glycine max), 3'ss of exon 8
-----gtgaacgtttttgcttgagtaccttgtctcctacgtatg---tatcgcaat-----atctcttccactgactggtaggctttcc-----ttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTTGTTAAGCGTGGCATGGAAGTGTTTGTTGCACAATCTTACAGCAAGAACC
      || |  |  ||   | |  |     |||  | |  |     ||| |  |      | || ||   |    || |   ||   |     |||||||| ||||| ||||||||||||||||||||||||  |||||| || || |||||    ||||||||||| ||  |||| || ||||||||||| || || |
tggaattggagttgattctataaaaattaaatctaatccaaacaccctatagagacctggaacctatttagcaacatgatgaactcctcattaattttagGGGTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCTTCTGTGAGACTGTTTGTGGCACGTGGCATGGAGGTTCTTGTAGCTCAATCTTACAGTAAAAATC

upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 8
-------------gtgaacgtttttgcttgagtaccttgtct-cctacgtatgtatcgcaatatctcttccactgactggtaggctttcc-----ttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTTGTTAAGCGTGGCATGGAAGTGTTTGTTGCACAATCTTACAGCAAGAACC
              | ||   |  | |      ||  | |    ||   ||   | |  |  | || ||   |    || |   ||   |     |||||||| ||||| ||||||||||||||||||||||||  |||||| || || |||||    |||||||| || ||  |||| || ||||||||||| || || |
tgattctagaaaaattaaatctaatccaaacacacactattaatctttatagagacc-tagaacctattttgcaacatgctgaactcctcattaattttagGGGTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCTTCTGTGAGACTGTTTGTGGCACGTGGCATCGAGGTTCTTGTAGCTCAATCTTACAGTAAAAATC

upper sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 9
--------gtgaacgtttttgcttgagtaccttgtctcctacgtatgtat-cgcaat-atctcttccactgactggtaggctttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTTGTTAAGCGTGGCATGGAAGTGTTTGTTGCACAATCTTACAGCAAGAACC
         |   | |   |    || || | ||| ||| |   | |||  || ||  || |  |  |  |     |   | |   ||  |||| ||||| ||||||||||||||||||||||||   ||||| ||  | |||| | |||| || |||||  | |||||||| || || || || || ||  
gtatccccctattcctacatttccgaatatcgtgtttccgagagaagtaagcgaaaccatattatgtaacgctacatgcacctattttccagGGCTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCATCTGTGAGATTATTTGCTGAGCGGGGAATGGAGTTTTTTGTTGCTCAGTCATATAGTAAAAATT

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|32845644|gb|CD985325.1|CD985325
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAA                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|26557436|gb|CA829671.1|CA829671
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAG                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32863795|gb|CF003477.1|CF003477
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAA                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|78104307|gb|DV522725.1|DV522725
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAG                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|5342983|gb|AI795288.1|AI795288
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAA                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32844188|gb|CD983869.1|CD983869
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAA                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32921476|gb|CF026288.1|CF026288
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAG                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32926958|gb|CF031770.1|CF031770
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAA                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32920753|gb|CF025565.1|CF025565
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAG                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32843721|gb|CD983402.1|CD983402
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAA                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32925729|gb|CF030541.1|CF030541
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAA                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32921723|gb|CF026535.1|CF026535
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAG                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGTATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|13150003|gb|BG320325.1|BG320325
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAG                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32843163|gb|CD982844.1|CD982844
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAA                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32921739|gb|CF026551.1|CF026551
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAG                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32925063|gb|CF029875.1|CF029875
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAA                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|6827402|gb|AW331045.1|AW331045
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAG                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32925965|gb|CF030777.1|CF030777
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAA                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|32925664|gb|CF030476.1|CF030476
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAA                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|91056033|gb|EB166451.1|EB166451
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAG                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
EST: gi|26557367|gb|CA829602.1|CA829602
EST:     ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAG                         GGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT
genomic: ATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTT

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), 47 (downstream exon)
Score: 107

CAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTTGTTAAGCGTGGCATGGAAGTGTTTGTTGCACAATCTTACAGCAAGAACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 592

CAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTTGTTAAGCGTGGCATGGAAGTGTTTGTTGCACAATCTTACAGCAAGAACC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 119

CAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTTGTTAAGCGTGGCATGGAAGTGTTTGTTGCACAATCTTACAGCAAGAACC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 309

CAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtgaacgttt ... ttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTTGTTAAGCGTGGCATGGAAGTGTTTGTTGCACAATCTTACAGCAAGAACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcctacgtatgtatcgcaatatctcttccactgactggtaggctttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTTGTTAAGCGTGGCATGGAAGTGTTTGTTGCACAATCTTACAGCAAGAACC
                             cactgac  putative branch site (score: 309)
                                           ctttcctttt  putative PPT
        tatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaacgtttttgcttgagtaccttgtctcctacgtatgtatcgcaatatctcttccactgactggtaggctttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTTGTTAAGCGTGGCATGGAAGTGTTTGTTGCACAATCTTACAGCAAGAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC