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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatcatctaatctctgttcaatcttcttcctggaaaaagtgagttactgaaagtgtgtcgtgataactgtgttgctgaaatttgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACCTGCCTGAGGCTAAGAATCTGAAGTCCTG

Basic information

species Zea mays
transcript GRMZM2G086934_T01
intron # 7
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|32944972|gb|CF049791.1|CF049791
EST:     CAGTTCTCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAG                         GCGTGTCTCTTTCAACTATTGGCAGAAGT
genomic: CAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAGgtacatcatc ... tgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGT
EST: gi|67023291|gb|CO452040.1|CO452040
EST:     CAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAG                         GTGTGTCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACC
genomic: CAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAGgtacatcatc ... tgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACC
EST: gi|61118644|gb|DN559605.1|DN559605
EST:     AGTTCGCCTGTTGTTGCGATAAAGAGCATAAGGGGTATCTGACTTCCAAG                         GCGTGTCTCTT
genomic: AGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAG-TATCTGACTTCCAAGgtacatcatc ... tgtgttgtagGCGTATCTCTT
EST: gi|32825102|gb|CD964824.1|CD964824
EST:     CAGTTCTCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAG                         GCGTGTCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTA
genomic: CAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAGgtacatcatc ... tgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTA
EST: gi|32943914|gb|CF048733.1|CF048733
EST:     CAGTTCTCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAG                         GCGTGTCTCTTTCAACTATTGGCAGAAGT
genomic: CAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAGgtacatcatc ... tgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGT
EST: gi|211282783|gb|FL192974.1|FL192974
EST:     CAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAG                         GCGTGTCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACC
genomic: CAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAGgtacatcatc ... tgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACC
EST: gi|61118643|gb|DN559604.1|DN559604
EST:     CAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAG                         GCGTGTCTCTTTCAACTATTGGCAGAAGTACT
genomic: CAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAGgtacatcatc ... tgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGTACT
EST: gi|32914104|gb|CF018916.1|CF018916
EST:     CAGTTCTCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAG                         GCGTGTCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACT
genomic: CAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAGgtacatcatc ... tgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACC

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: 765

TGGAATGATCTTGCTACTACGACTGGCCAAGAGCTTTTGGACATGGTTGACAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAGgtacatcatc ... tgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACCTGCCTGAGGCTAAGAATCTGAAGTCCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 142

TGGAATGATCTTGCTACTACGACTGGCCAAGAGCTTTTGGACATGGTTGACAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAGgtacatcatc ... tgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACCTGCCTGAGGCTAAGAATCTGAAGTCCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 120

TGGAATGATCTTGCTACTACGACTGGCCAAGAGCTTTTGGACATGGTTGACAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAGgtacatcatc ... tgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACCTGCCTGAGGCTAAGAATCTGAAGTCCTG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 37

TGGAATGATCTTGCTACTACGACTGGCCAAGAGCTTTTGGACATGGTTGACAGTTCGCCTGTTGTTGCGATAAAGAGCCTAAAAGTATCTGACTTCCAAGgtacatcatc ... tgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACCTGCCTGAGGCTAAGAATCTGAAGTCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgagttactgaaagtgtgtcgtgataactgtgttgctgaaatttgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACCTGCCTGAGGCTAAGAATCTGAAGTCCTG
                       tgataac  putative branch site (score: 37)
                                      tgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatcatctaatctctgttcaatcttcttcctggaaaaagtgagttactgaaagtgtgtcgtgataactgtgttgctgaaatttgtgttgtagGCGTATCTCTTTCAACTATTGGCAGAAGTACTCTCGAGATTAATCCTGACCTGCCTGAGGCTAAGAATCTGAAGTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG