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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctaaagccccctttatccgcgccaaatctcttcctcccaaatcgtcgttaattgttatgtatgccattttcttcatctacaaatttcgattgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG

Basic information

species Zea mays
transcript GRMZM2G177273_T01
intron # 1
splice site 3'
intron type U2

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|5439423|gb|AI820344.1|AI820344
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|211489479|gb|FL115189.1|FL115189
EST:     CTTCCTTGCCGCCGGAG-ACGG-ATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|76915127|gb|DV165838.1|DV165838
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|211489485|gb|FL115195.1|FL115195
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAA
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAA
EST: gi|32937240|gb|CF042059.1|CF042059
EST:     CTTCCTTGCCGCCGGAGGACGACATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|211489484|gb|FL115194.1|FL115194
EST:     TTCCTTGCCGCCGGA-GACGGCATTCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: TTCCTTGCCGCCGGAGGACGGCA-TCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|5566736|gb|AI881602.1|AI881602
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|211489482|gb|FL115192.1|FL115192
EST:     TTCCTTGCCGCCGGA-GACGG-ATTCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: TTCCTTGCCGCCGGAGGACGGCA-TCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|211489481|gb|FL115191.1|FL115191
EST:     TTCCTTGCCGCCGGA-GACGG-ATTCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: TTCCTTGCCGCCGGAGGACGGCA-TCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|91055996|gb|EB166414.1|EB166414
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|211489476|gb|FL115186.1|FL115186
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|71440146|gb|DR821196.1|DR821196
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|74236701|gb|DT644615.1|DT644615
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|211489478|gb|FL115188.1|FL115188
EST:     CTTCCTTGCCGCCGGA-GACGGSATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|74240661|gb|DT648575.1|DT648575
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|211489483|gb|FL115193.1|FL115193
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|211489475|gb|FL115185.1|FL115185
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|211489480|gb|FL115190.1|FL115190
EST:     CTTCCTTGCCGCCGGA-GACGG-ATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|71434958|gb|DR816008.1|DR816008
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|78075802|gb|DV504236.1|DV504236
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|5268817|gb|AI770781.1|AI770781
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|211489477|gb|FL115187.1|FL115187
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|89251976|gb|DY623762.1|DY623762
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|78085357|gb|DV513750.1|DV513750
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
EST: gi|71449605|gb|DR830655.1|DR830655
EST:     CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGA                         ATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
genomic: CTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG

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: 262

AGCCACCCGTGCCCTCCTCCTGCTCGTCATCGCGTCCGCCGTTTCCTGCTCTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 262

AGCCACCCGTGCCCTCCTCCTGCTCGTCATCGCGTCCGCCGTTTCCTGCTCTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG


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

AGCCACCCGTGCCCTCCTCCTGCTCGTCATCGCGTCCGCCGTTTCCTGCTCTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 274

AGCCACCCGTGCCCTCCTCCTGCTCGTCATCGCGTCCGCCGTTTCCTGCTCTTCCTTGCCGCCGGAGGACGGCATCCGGGTCGTCTCTGCAGAGAAAAGAgtatgtatgc ... ttgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgttaattgttatgtatgccattttcttcatctacaaatttcgattgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG
 cgttaat  putative branch site (score: 274)
     aattgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctaaagccccctttatccgcgccaaatctcttcctcccaaatcgtcgttaattgttatgtatgccattttcttcatctacaaatttcgattgcctgcagATCGACCTCACGGGTCCCATCGTCAAAGTCTTCCTAACATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtatg