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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttccttgtatcttaagcatctttctacaagagaatctatgatagcttataggttttgtcatataactaatgttctttctttgttctgttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG

Basic information

species Zea mays
transcript GRMZM2G021864_T01
intron # 15
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|33091337|gb|CF051331.1|CF051331
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|78022987|gb|DV491374.1|DV491374
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|32931903|gb|CF036715.1|CF036715
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|211458170|gb|FL127582.1|FL127582
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|89248917|gb|DY620703.1|DY620703
EST:     ATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|89758497|gb|DY687658.1|DY687658
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|211460681|gb|FL127583.1|FL127583
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|32934210|gb|CF039022.1|CF039022
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|78106767|gb|DV525185.1|DV525185
EST:     CAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: CAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|32912991|gb|CF017803.1|CF017803
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGGGCTGATCAAGCACAAGAGAACAATTATGGACTC
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGT-CTGATCAAGCACAAGAGAACAAT-ATGGACTC
EST: gi|211460682|gb|FL127584.1|FL127584
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|32930527|gb|CF035339.1|CF035339
EST:     ACTACCAGAGACATATGTCGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCGCAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|5915604|gb|AW053245.1|AW053245
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|32932800|gb|CF037612.1|CF037612
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|5361116|gb|AI795731.1|AI795731
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|32932808|gb|CF037620.1|CF037620
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|91054831|gb|EB165249.1|EB165249
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|13381810|gb|BG458485.1|BG458485
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTNNNNNNNNNNATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
EST: gi|12968788|gb|BG265825.1|BG265825
EST:     ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATG                         GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG
genomic: ACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAG

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), 49 (downstream exon)
Score: 168

CACCATAAAGCTTCCAGTGTCCGAAGAACTGGAGGGCTTTCGTCAAATTTACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 75

CACCATAAAGCTTCCAGTGTCCGAAGAACTGGAGGGCTTTCGTCAAATTTACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

CACCATAAAGCTTCCAGTGTCCGAAGAACTGGAGGGCTTTCGTCAAATTTACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 86

CACCATAAAGCTTCCAGTGTCCGAAGAACTGGAGGGCTTTCGTCAAATTTACTACCAGAGACATATGACGACATAACAACTGTTGGGTTAGCAAATAATGgtgctcaata ... ttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttataggttttgtcatataactaatgttctttctttgttctgttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG
                     aactaat  putative branch site (score: 86)
                           tgttctttctttgttc  CT-rich tract
                 atataactaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttccttgtatcttaagcatctttctacaagagaatctatgatagcttataggttttgtcatataactaatgttctttctttgttctgttttggccagGTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - cttgtat