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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgccacctaaccaacttagctagagcctcgttcgcatgcactttatggattctaaatcatttttttgaatatattgttggtacttattaccgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAAAGTTCGAGGATGGGAG

Basic information

species Zea mays
transcript GRMZM2G135132_T01
intron # 9
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|4775994|gb|AI664997.1|AI664997
EST:     GCTCCCTTCATCTGTGAGTTTTTCTGTGATGCCCAAGAGAAGGTCCTCCC                         GTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
genomic: GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCCgtaagtctta ... accgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
EST: gi|211535004|gb|FL000873.1|FL000873
EST:     CATCC-TTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCC                         GTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCACAAATCTTTCGC-A
genomic: C-TCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCCgtaagtctta ... accgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTT-CGCCA
EST: gi|60340226|gb|DN207199.1|DN207199
EST:     GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCC                         GTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
genomic: GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCCgtaagtctta ... accgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
EST: gi|211259748|gb|FL311234.1|FL311234
EST:     GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCC                         GTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
genomic: GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCCgtaagtctta ... accgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
EST: gi|60355835|gb|DN222808.1|DN222808
EST:     GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCC                         GTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
genomic: GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCCgtaagtctta ... accgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
EST: gi|60337076|gb|DN204049.1|DN204049
EST:     GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCC                         GTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
genomic: GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCCgtaagtctta ... accgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
EST: gi|31353988|gb|CD438345.1|CD438345
EST:     GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCC                         GTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
genomic: GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCCgtaagtctta ... accgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
EST: gi|60395531|gb|DN228401.1|DN228401
EST:     GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCC                         GTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA
genomic: GCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCCgtaagtctta ... accgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAA

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), 32 (downstream exon)
Score: 942

GTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCCgtaagtctta ... accgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAAAGTTCGAGGATGGGAG


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 1039

GTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCCgtaagtctta ... accgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAAAGTTCGAGGATGGGAG


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 1024

GTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCCgtaagtctta ... accgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAAAGTTCGAGGATGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1407

GTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCCgtaagtctta ... accgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAAAGTTCGAGGATGGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggattctaaatcatttttttgaatatattgttggtacttattaccgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAAAGTTCGAGGATGGGAG
      ttctaaa  putative branch site (score: 1407)
     attctaaatcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgccacctaaccaacttagctagagcctcgttcgcatgcactttatggattctaaatcatttttttgaatatattgttggtacttattaccgatatagGTATGCTGACTTCATCTTCGGCAATGAAACCGAGGCAAAAATCTTCGCCAAAGTTCGAGGATGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- -gccacct
- - - - - aaccaac
- - - - - - - - - - - - - - - - - cgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttggt