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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgtcttatctgttttaattgggctggagcaagcaagatttatagggtttagtttgattgtctattttgctaccaacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCG

Basic information

species Zea mays
transcript GRMZM2G108829_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|211109867|gb|FL467764.1|FL467764
EST:     CGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: CGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|86469589|gb|DY235959.1|DY235959
EST:     CATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: CATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|78078782|gb|DV507194.1|DV507194
EST:     GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|60349468|gb|DN216441.1|DN216441
EST:     GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAA
genomic: GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAA
EST: gi|211262786|gb|FL340148.1|FL340148
EST:     CGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: CGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|84980182|gb|DW530531.1|DW530531
EST:     GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|78022750|gb|DV491137.1|DV491137
EST:     GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|211188910|gb|FL465389.1|FL465389
EST:     CGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: CGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|40334857|gb|CK368927.1|CK368927
EST:     AATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: AATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|37378370|gb|CF625872.1|CF625872
EST:     AAAT-GTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: AAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|5770191|gb|AI973365.1|AI973365
EST:     GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|211496287|gb|FL041699.1|FL041699
EST:     GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|32870331|gb|CF010013.1|CF010013
EST:     GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|211308763|gb|FL367424.1|FL367424
EST:     CGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: CGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|5325074|gb|AI783265.1|AI783265
EST:     GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|5846886|gb|AI999969.1|AI999969
EST:     GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|87155121|gb|DY399910.1|DY399910
EST:     GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|15215165|gb|BI431185.1|BI431185
EST:     GAAATCCCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
EST: gi|60358960|gb|DN225933.1|DN225933
EST:     GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTG                         GTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA
genomic: GAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGA

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: 298

TCAGAGAACAGTGTGGCTAGAAGATTCTCAACTGGAACTCTATCTACAATGAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

TCAGAGAACAGTGTGGCTAGAAGATTCTCAACTGGAACTCTATCTACAATGAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

TCAGAGAACAGTGTGGCTAGAAGATTCTCAACTGGAACTCTATCTACAATGAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

TCAGAGAACAGTGTGGCTAGAAGATTCTCAACTGGAACTCTATCTACAATGAAATCTCATAGCAATGCATCCGCAAAATTAAATGGTTTATCTAAGACTGgtgcgtgtct ... aacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagcaagatttatagggtttagtttgattgtctattttgctaccaacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCG
                      gtttgat  putative branch site (score: 221)
     aagatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgtcttatctgttttaattgggctggagcaagcaagatttatagggtttagtttgattgtctattttgctaccaacattacagGTGTACAAAGAAAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC