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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgatttttttcttttgaataaacccacttttagttatattgattgattgaagggacacttatcattctttactttaatggtgcactacttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACAAGTTTTGATTAGACTAGAAGACAGCATCATATTTGGACTTTTGGAGAGA

Basic information

species Zea mays
transcript GRMZM2G116087_T01
intron # 2
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|148966792|gb|EE017885.2|EE017885
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|149029771|gb|EE286265.2|EE286265
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|148973538|gb|EE024639.2|EE024639
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|211279057|gb|FK954642.1|FK954642
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|148938252|gb|EC882544.2|EC882544
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|149088482|gb|EE177591.2|EE177591
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|28873742|gb|CB329688.1|CB329688
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|78089260|gb|DV517634.1|DV517634
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|94479717|gb|EB708675.1|EB708675
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|211029807|gb|FL058985.1|FL058985
EST:     AKGAACAAGGGGCTCCGCACGGCRAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|211466167|gb|FL380586.1|FL380586
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|78111571|gb|DV529968.1|DV529968
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|148952137|gb|EC897931.2|EC897931
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|71448582|gb|DR829632.1|DR829632
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|149086680|gb|EE176220.2|EE176220
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
EST: gi|148961522|gb|EE012274.2|EE012274
EST:     AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCACGGCCAACAACTCCGCAACGCCCATGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattgaagggacacttatcattctttactttaatggtgcactacttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACAAGTTTTGATTAGACTAGAAGACAGCATCATATTTGGACTTTTGGAGAGA
                             ctttaat  putative branch site (score: 4)
                                          ctactttt  putative PPT
                     attctttactttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgatttttttcttttgaataaacccacttttagttatattgattgattgaagggacacttatcattctttactttaatggtgcactacttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATCAGACAAGTTTTGATTAGACTAGAAGACAGCATCATATTTGGACTTTTGGAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA