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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaagcctttcctcttctttttctatttataatgccctcagattgaagcattctacatctcaaaaattctgcattggatcccttatttgcaaatttatgccgacaggcggcatcattgtttgctctgttgcagttcactttgtgctaagatgtgcatcttgcag

Basic information

species Zea mays
transcript GRMZM2G000718_T01
intron # 4
splice site 5'
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|211216370|gb|FL354222.1|FL354222
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAG-CCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTA
EST: gi|28361821|gb|CB240177.1|CB240177
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211142613|gb|FL363442.1|FL363442
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACT
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACT
EST: gi|211028706|gb|FL343658.1|FL343658
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211108631|gb|FL325828.1|FL325828
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATMAAGAGGATCGAACTATTCGATACGGGTA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAAT-AAGAGGATCGAACTATTCGATACGGGTA
EST: gi|149002889|gb|EE038886.2|EE038886
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211049854|gb|FL341783.1|FL341783
EST:     ATCAAAGANCTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCG
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCG
EST: gi|148941490|gb|EC886419.2|EC886419
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|21843414|gb|BQ703995.1|BQ703995
EST:     ATCAAAGAACTCAACTCCTATGTAACCTTGAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGGTCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|37420501|gb|CF647941.1|CF647941
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211541608|gb|FL367257.1|FL367257
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|33466594|gb|CF243643.1|CF243643
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|71327359|gb|DR800293.1|DR800293
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211440064|gb|FL316511.1|FL316511
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGT
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGT
EST: gi|148993116|gb|EE033716.2|EE033716
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211164059|gb|FL355972.1|FL355972
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTGAGGAAAAC                         GTACCAGAGCCGCCTTGGTAATAAGAGGATCGAACTATTCGAATACGG-TA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGA-TACGGGTA
EST: gi|149112851|gb|EE295664.2|EE295664
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|60352046|gb|DN219019.1|DN219019
EST:     GTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: GTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|149009782|gb|EE041679.2|EE041679
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|78117925|gb|DV536312.1|DV536312
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211067349|gb|FL342683.1|FL342683
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211037667|gb|FL309759.1|FL309759
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|149089650|gb|EE178904.2|EE178904
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|78083753|gb|DV512146.1|DV512146
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211285641|gb|FL366666.1|FL366666
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211510365|gb|FL349271.1|FL349271
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAA-C                         GTACCAGAGCAGC
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGC
EST: gi|211162036|gb|FL334323.1|FL334323
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAAYAAGAGGATCGAACTATTCGATACGGG
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGG
EST: gi|211100818|gb|FL317193.1|FL317193
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTGAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAAGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|91869534|gb|EB400432.1|EB400432
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211125915|gb|FL330703.1|FL330703
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGGAAAAC                         GTACCAGAGCAG
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGG-AAAACgtaagtacaa ... catcttgcagGTACCAGAGCAG
EST: gi|30088413|gb|CB886618.1|CB886618
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211512069|gb|FL314329.1|FL314329
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTA-GGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGT
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGT
EST: gi|28361634|gb|CB239990.1|CB239990
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211262335|gb|FL317743.1|FL317743
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATC
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATC
EST: gi|211314807|gb|FL364565.1|FL364565
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAG
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAG
EST: gi|211411458|gb|FL312810.1|FL312810
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|149074291|gb|EE162669.2|EE162669
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|50333644|gb|CO528770.1|CO528770
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211190651|gb|FL327243.1|FL327243
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|26456321|gb|CA827904.1|CA827904
EST:     ATCAAAGAACTCAACTCCTATGTAACCTTGAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGGTCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211477883|gb|FL341268.1|FL341268
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTTT
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTA-
EST: gi|20301313|gb|BQ164256.1|BQ164256
EST:     ATCAAAGAACTCAACTCCTATGTAACCTTGAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGAGGGTCGAACTATTCGATACGGGTAA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAA
EST: gi|211018150|gb|FL327162.1|FL327162
EST:     ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAAC                         GTACCAGAGCAGCCTTGGTAATAAGA
genomic: ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGA

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: 38 (upstream exon), 48 (downstream exon)
Score: 276

ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 171

ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 93

ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 167

ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaa ... catcttgcagGTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAAAGAACTCAACTCCTATGTGACCTTAAGGAAAACgtaagtacaagcctttcctcttctttttctatttataatgccctcagattgaagcattctacatctcaaaaattctgcattggatcccttatttgcaaatttatgccgacaggcggcatcattgtttgctctgttgcagttcactttgtgctaagatgtgcatcttgcag

-  AAAGAA
- - AAGAAC
- - - - - - - - - - - - - -  AAGGAA