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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgtgatcatgtatattagactgcagtgcattccttatgtgttgcttactacaccactgacagccttgcgctctgcgcgttggagaaagctaacaagtaaatattcatcgtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG

Basic information

species Zea mays
transcript GRMZM2G553379_T07
intron # 4
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|71316728|gb|DR795038.1|DR795038
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCA
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCA
EST: gi|18659149|gb|BM500180.1|BM500180
EST:     ACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATTCAGAACCAGGAAG                         AACCAACTTTATGCTCGAGTTCAATT
genomic: ACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATAT-CAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTT-ATGCTCGAGT-CAATT
EST: gi|50323594|gb|CO518720.1|CO518720
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAA
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAA
EST: gi|67016868|gb|CO445617.1|CO445617
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCA-CGGAAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAA-G
EST: gi|78081870|gb|DV510282.1|DV510282
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
EST: gi|148980413|gb|EE027124.2|EE027124
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGAAAG                         AACCTACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
EST: gi|88748868|gb|DY533009.1|DY533009
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
EST: gi|78081869|gb|DV510281.1|DV510281
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
EST: gi|76280608|gb|DV020176.1|DV020176
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
EST: gi|76292653|gb|DV032221.1|DV032221
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTTCG-AGCTCAAACGGAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTT-CGGAGCTCCAACGGAAG
EST: gi|78082314|gb|DV510726.1|DV510726
EST:     ACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCCAGGAAG                         ACCCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAGG
genomic: ACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACC-AGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAGG
EST: gi|71325989|gb|DR799677.1|DR799677
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCC
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCC
EST: gi|76935540|gb|DV174367.1|DV174367
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
EST: gi|50325811|gb|CO520937.1|CO520937
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
EST: gi|149001052|gb|EE038303.2|EE038303
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
EST: gi|74242354|gb|DT650268.1|DT650268
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAA
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAA
EST: gi|26559940|gb|CA832175.1|CA832175
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACAGAAGGA
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAGGA
EST: gi|78088356|gb|DV516749.1|DV516749
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCTACGNAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
EST: gi|211264632|gb|FL311268.1|FL311268
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACAGAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
EST: gi|89757241|gb|DY686923.1|DY686923
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGC
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGC
EST: gi|76927299|gb|DV171231.1|DV171231
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
EST: gi|149083438|gb|EE172758.2|EE172758
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCANGAAG                         AACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
EST: gi|74244253|gb|DT652167.1|DT652167
EST:     AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG                         AACCAACTTATGCTCGAGT
genomic: AACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGT

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: 48 (upstream exon), 42 (downstream exon)
Score: 220

GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCAACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG


Block sizes: 46 (upstream exon), 42 (downstream exon)
Score: 168

GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCAACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAGgtagtgtgat ... gtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcgctctgcgcgttggagaaagctaacaagtaaatattcatcgtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG
                       agctaac  putative branch site (score: 168)
                          taacaagtaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgtgatcatgtatattagactgcagtgcattccttatgtgttgcttactacaccactgacagccttgcgctctgcgcgttggagaaagctaacaagtaaatattcatcgtatgcgcagAACCAACTTATGCTCGAGTCAATTTCGGAGCTCCAACGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT