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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catctaattgtgcatgtctcatcgctacttgcctactttataattactaaaactcatatcaaggtgccataattttatctgtctgatatttactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG

Basic information

species Zea mays
transcript GRMZM2G161087_T01
intron # 16
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|32934996|gb|CF039808.1|CF039808
EST:     CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTG                         GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
genomic: CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGgtaatttcct ... tactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
EST: gi|32931261|gb|CF036073.1|CF036073
EST:     CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTG                         GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
genomic: CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGgtaatttcct ... tactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
EST: gi|32933316|gb|CF038128.1|CF038128
EST:     CCAGTGGACTGATAGAATGAGAGAGGGTCAGAACTAAATCCCAGCCATTG                         GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
genomic: CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGgtaatttcct ... tactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
EST: gi|26559353|gb|CA831588.1|CA831588
EST:     AGGGTCAGAACTAAATCCCAGCCATTG                         GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
genomic: AGGGTCAGAACTAAATCCCAGCCATTGgtaatttcct ... tactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
EST: gi|32934128|gb|CF038940.1|CF038940
EST:     CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTG                         GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
genomic: CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGgtaatttcct ... tactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
EST: gi|113701833|gb|EE679337.1|EE679337
EST:     CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTG                         GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
genomic: CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGgtaatttcct ... tactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
EST: gi|32932425|gb|CF037237.1|CF037237
EST:     CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTG                         GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
genomic: CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGgtaatttcct ... tactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
EST: gi|71772591|gb|DR970520.1|DR970520
EST:     CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTG                         GACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG
genomic: CCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGgtaatttcct ... tactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAG

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), 48 (downstream exon)
Score: 232

AAACCGAAAATTGTTTCAAAATGGCAGTACTGGTTTGATAACACCTCAATCCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGgtaatttcct ... tactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 90

AAACCGAAAATTGTTTCAAAATGGCAGTACTGGTTTGATAACACCTCAATCCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGgtaatttcct ... tactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

AAACCGAAAATTGTTTCAAAATGGCAGTACTGGTTTGATAACACCTCAATCCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGgtaatttcct ... tactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 105

AAACCGAAAATTGTTTCAAAATGGCAGTACTGGTTTGATAACACCTCAATCCAGTGGACTGATAGAAAGAGAGAGGGTCAGAACTAAATCCCAGCCATTGgtaatttcct ... tactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaaaactcatatcaaggtgccataattttatctgtctgatatttactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG
                       ataattttatctgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catctaattgtgcatgtctcatcgctacttgcctactttataattactaaaactcatatcaaggtgccataattttatctgtctgatatttactgcccagGACCCAAAAGCAACAAGCAACGGAGATCTACATACTATGGATGAGTATCAGTCTGTTATCATGCAGTTAAGGGATGAAAATTCATCACTAAAGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - tgcatgt
- - - - - - - - - - - - -tacttgc
- - - - - - - - - - - - - - - - - - - - - - - - -aaactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgcca