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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctactattttagatttatgtaattatgcaccacagtggatttgtatgagtttcgttccacaagctaagctctagtttccttgatgatttaaaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTTAGGCTTACAATGAATATACTGCGGTCTGTTGTCAATGGGGATGTTTATG

Basic information

species Zea mays
transcript GRMZM2G042818_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042818_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g54860.1 (Oryza sativa), 3'ss of exon 11
ctactattttagatttatgtaattatgcaccacagtggatttgtatgagtttcgttccacaagctaag-------ctctagtttccttgatgatttaaaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTTAGGCTTACAATGAATATACTGCGGTCTGTTGTCAATGGGGATGTTTATG
     ||||| ||   || |  ||||| |     ||| ||||  | |    |  || ||||||  |||          || | |   || |  ||| || | ||||||||||||||||||| || |||||  |||| ||||||||||  ||||||||  | ||||||||||| |  || || ||||| || | ||| ||||| ||||
----aatttttgac--atcttgttatgtattgtggtgcatttaca-gctcctttttgcacaaggcaagaatgtattcttaatattaatggttgttttaattcttcagATCAGAGAAGGTCGGAAGCAGAGCCTGCCGGAATGTTTGAAGAAGGAATTCCGACTTACAATGAACACTCTCCGATCTGTAGTTACTGGCGATGTCTATG
















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|74240479|gb|DT648393.1|DT648393
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|29544823|gb|CB605431.1|CB605431
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|37400624|gb|CF637668.1|CF637668
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|15057208|gb|BI361180.1|BI361180
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|15177481|gb|BI398420.1|BI398420
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGT
EST: gi|148959114|gb|EC905254.2|EC905254
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGATTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|45568357|gb|CK986026.1|CK986026
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|37392700|gb|CF633603.1|CF633603
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATCGTTTGACTAAGGAATT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAAT-GTTTGACTAAGGAATT
EST: gi|20336949|gb|BQ172579.1|BQ172579
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|45847757|gb|CN071700.1|CN071700
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGGTCGCCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|33092056|gb|CF052050.1|CF052050
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|32930057|gb|CF034869.1|CF034869
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|71304194|gb|DR788217.1|DR788217
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|29544214|gb|CB604594.1|CB604594
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|37383733|gb|CF628896.1|CF628896
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|40303747|gb|CK348134.1|CK348134
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|91053743|gb|EB164161.1|EB164161
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGATTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|74239819|gb|DT647733.1|DT647733
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|211149870|gb|FL475634.1|FL475634
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|37379687|gb|CF626591.1|CF626591
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
EST: gi|71762792|gb|DR960729.1|DR960729
EST:     AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG                         ATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT
genomic: AGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 258

GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTTAGGCTTACAATGAATATACTGCGGTCTGTTGTCAATGGGGATGTTTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 487

GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTTAGGCTTACAATGAATATACTGCGGTCTGTTGTCAATGGGGATGTTTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 386

GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTTAGGCTTACAATGAATATACTGCGGTCTGTTGTCAATGGGGATGTTTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 890

GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCGgtacagtctc ... aaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTTAGGCTTACAATGAATATACTGCGGTCTGTTGTCAATGGGGATGTTTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtttcgttccacaagctaagctctagtttccttgatgatttaaaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTTAGGCTTACAATGAATATACTGCGGTCTGTTGTCAATGGGGATGTTTATG
                                ccttgat  putative branch site (score: 890)
                                                ttttc  putative PPT
                                  ttgatgatttaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctactattttagatttatgtaattatgcaccacagtggatttgtatgagtttcgttccacaagctaagctctagtttccttgatgatttaaaattttcagATCAGAGAAGGTCGAAAACAGAGTTTGCCTGAATGTTTGACTAAGGAATTTAGGCTTACAATGAATATACTGCGGTCTGTTGTCAATGGGGATGTTTATG

- - - - - - - - - - - - - -caccaca
- - - - - - - - - - - - - - - - - - - - ttgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgat