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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgaccgcgcgtgttaattccaagcatctgctagctgctctgctgctagttcgggatcttcttcttcatgcatgcatttcatgatcatatatgtatctccttgagaccttcttgacggcatatatatgtatatgtacatgcatcatgcatcgaccgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCGCAGGTGTCCGCGGCCGTGACCTACCATGGCAAGAGCTCCAGCAGCAACA

Basic information

species Zea mays
transcript GRMZM2G162200_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|211069490|gb|FL200214.1|FL200214
EST:     AAAAAGCACAAGAWATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211069483|gb|FL200207.1|FL200207
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211072227|gb|FL200227.1|FL200227
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211069492|gb|FL200216.1|FL200216
EST:     AAAAGCACAAGAWATGGCGGCCG-CTTCTCCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAGCACAAGAAATGGCGGCCGCCTTCT-CCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|15545696|gb|BI643490.1|BI643490
EST:     AAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211069493|gb|FL200217.1|FL200217
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|32921691|gb|CF026503.1|CF026503
EST:     GCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: GCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|149095830|gb|EE181481.2|EE181481
EST:     CTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: CTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|32920574|gb|CF025386.1|CF025386
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCCCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCG
EST: gi|211069486|gb|FL200210.1|FL200210
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211069488|gb|FL200212.1|FL200212
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|148943452|gb|EC888511.2|EC888511
EST:     CTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: CTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|15590453|gb|BI675069.1|BI675069
EST:     CTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: CTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211069494|gb|FL200218.1|FL200218
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCTTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211072225|gb|FL200225.1|FL200225
EST:     AAAAAGCACAAGAWATGGCGGCCG-CTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211072224|gb|FL200224.1|FL200224
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211072220|gb|FL200220.1|FL200220
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211069489|gb|FL200213.1|FL200213
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211069487|gb|FL200211.1|FL200211
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211072221|gb|FL200221.1|FL200221
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211069495|gb|FL200219.1|FL200219
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211072223|gb|FL200223.1|FL200223
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|148994664|gb|EE034185.2|EE034185
EST:     GGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: GGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|148939916|gb|EC884636.2|EC884636
EST:     CTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: CTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211072229|gb|FL200229.1|FL200229
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|149105461|gb|EE290977.2|EE290977
EST:     CTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: CTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|13126318|gb|BG316888.1|BG316888
EST:     ATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGCAAGAAGCTCAACAAGCC
genomic: ATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGG-AAGAAGCTCAACAAGCC
EST: gi|211069491|gb|FL200215.1|FL200215
EST:     CGGCCG-CTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: CGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|149100221|gb|EE186283.2|EE186283
EST:     GGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: GGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
EST: gi|211072226|gb|FL200226.1|FL200226
EST:     AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCG                         GCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG
genomic: AAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCG

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 473

CGTGTGCGTGCCTCGACGACCTCACTACTTTGAGCTGCAAGGTCCGAACTAAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCGCAGGTGTCCGCGGCCGTGACCTACCATGGCAAGAGCTCCAGCAGCAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

CGTGTGCGTGCCTCGACGACCTCACTACTTTGAGCTGCAAGGTCCGAACTAAAAAGCACAAGAAATGGCGGCCGCCTTCTCCTCCACCGTCGGAGCTCCGgtgggtgacc ... cgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCGCAGGTGTCCGCGGCCGTGACCTACCATGGCAAGAGCTCCAGCAGCAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgacggcatatatatgtatatgtacatgcatcatgcatcgaccgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCGCAGGTGTCCGCGGCCGTGACCTACCATGGCAAGAGCTCCAGCAGCAACA
 tcttgac  putative branch site (score: 202)
          atatatatgtatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgaccgcgcgtgttaattccaagcatctgctagctgctctgctgctagttcgggatcttcttcttcatgcatgcatttcatgatcatatatgtatctccttgagaccttcttgacggcatatatatgtatatgtacatgcatcatgcatcgaccgatcatcagGCCTCCACCCCGACCAGGAGCAGCTTCCTCGGGAAGAAGCTCAACAAGCCGCAGGTGTCCGCGGCCGTGACCTACCATGGCAAGAGCTCCAGCAGCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT