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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttcattttcctcgtcgtctttgttttttctctcttcattttttggaggaaaattttttgtgcaaagttccacatgtttcctgagctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGAGGATATGATAGAAAGGCTCATTGTGGAGTGTGACAGGAAAATTCAGAGG

Basic information

species Zea mays
transcript GRMZM2G069916_T02
intron # 2
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 2
gtatccttcattttcctcgtcgtctt-tgttttttctctcttcattttttggaggaaaattttttgtgcaaagttccacatgt-ttcctgagctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGAGGATATGATAGAAAGGCTCATTGTGGAGTGTGACAGGAAAATTCAGAGG
||||||||    ||      |   |  | ||| | || |    || ||  | |    | | | | | | | |||      ||  ||||||| ||||| | |||||||||||||  || ||||| ||||||||||||| |||||| ||||||||||| |||||||| |||||||| |||||||| || |||||||||||||||
gtatcctttgacttatggaacacttcatctttctccttttaaaatattccgcactctactgtatagagtatagtggtctttgccttcctgaactgttcgcagTTATGAAGAAGTAAAGGCAAAAGGAACAGAAAATTATGATAGGGAACTCGAGGAAATGATAGACAGGCTCATCGTGGAGTGCGAGAGGAAAATTCAGAGG
















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|211479946|gb|FL425922.1|FL425922
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCATTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAAGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|211423515|gb|FL160031.1|FL160031
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|67033512|gb|CO462261.1|CO462261
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCATTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|71330193|gb|DR801854.1|DR801854
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|148973852|gb|EE024993.2|EE024993
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|76292705|gb|DV032273.1|DV032273
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|211420922|gb|FL160021.1|FL160021
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAG
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAG
EST: gi|76920400|gb|DV168155.1|DV168155
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|149014011|gb|EE043527.2|EE043527
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|88756297|gb|DY540438.1|DY540438
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|148952947|gb|EE152420.2|EE152420
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|87157671|gb|DY402460.1|DY402460
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCATTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAAGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|211420926|gb|FL160025.1|FL160025
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|9731138|gb|BE509890.1|BE509890
EST:     ATGGATCTCGGTCCTTGCTCTAAGATTCATTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAAGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|148932069|gb|EC875423.2|EC875423
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|211420930|gb|FL160029.1|FL160029
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGGAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|71312972|gb|DR793008.1|DR793008
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|149000973|gb|EE038213.2|EE038213
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|88756334|gb|DY540475.1|DY540475
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAATAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGACAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|211420928|gb|FL160027.1|FL160027
EST:     ATGGATCTCGGTCCTTGTTCGAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|211024315|gb|FL368572.1|FL368572
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCATTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAAGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|211142603|gb|FL018649.1|FL018649
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA
EST: gi|9952467|gb|BE639050.1|BE639050
EST:     ATGGATCTCGGTCCTTGTTCTAAGATTCATTCTCTTCAACTGCGGAAAGA                         TTATGAAGAAGCGAAAGCAAAAGGAACAGAAAATTTTGATAGAGAACTCGA
genomic: ATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 294

AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGAGGATATGATAGAAAGGCTCATTGTGGAGTGTGACAGGAAAATTCAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGAGGATATGATAGAAAGGCTCATTGTGGAGTGTGACAGGAAAATTCAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 209

AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGAGGATATGATAGAAAGGCTCATTGTGGAGTGTGACAGGAAAATTCAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

AAAATGGATCTCGGTCCTTGTTCTAAGATTCACTCTCTTCAACTGCGGAAAGAgtatccttca ... ctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGAGGATATGATAGAAAGGCTCATTGTGGAGTGTGACAGGAAAATTCAGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggaggaaaattttttgtgcaaagttccacatgtttcctgagctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGAGGATATGATAGAAAGGCTCATTGTGGAGTGTGACAGGAAAATTCAGAGG
 ttcctgagc  putative branch site 
         aaaattttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttcattttcctcgtcgtctttgttttttctctcttcattttttggaggaaaattttttgtgcaaagttccacatgtttcctgagctgttggtagTTATGAAGAAGCGAAAGCAAAGGGAACAGAAAATTTTGATAGAGAACTCGAGGATATGATAGAAAGGCTCATTGTGGAGTGTGACAGGAAAATTCAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG