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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggtcttctattttgatttaatttcattgttgctggcacactttattctccatgttatgacttctcctaagatatccagctcctttcctacttggtttaagtacagttgttctgcag

Basic information

species Zea mays
transcript GRMZM2G136803_T01
intron # 7
splice site 5'
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|211541853|gb|FL147715.1|FL147715
EST:     GGGTAGAGAAAGAGGACAGTATCCGCCGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCGG
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCG-
EST: gi|32931864|gb|CF036676.1|CF036676
EST:     TGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCGT
genomic: TGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCG-
EST: gi|211541852|gb|FL147714.1|FL147714
EST:     GGGTAGAGAAAGAGGACAGTATCCGCCGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCGT
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCGT
EST: gi|211541851|gb|FL147713.1|FL147713
EST:     GGGTAGAGAAAGAGGACAGTATCCGACGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGG
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGG
EST: gi|32930164|gb|CF034976.1|CF034976
EST:     GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCGT
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCG-
EST: gi|32836690|gb|CD976368.1|CD976368
EST:     GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCGT
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCG-
EST: gi|211153097|gb|FL147716.1|FL147716
EST:     GGGTAGAGAAAGAGGACAGTATCCGCCGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGA
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGA
EST: gi|32932023|gb|CF036835.1|CF036835
EST:     TTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCGT
genomic: TTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCG-
EST: gi|78120827|gb|DV539211.1|DV539211
EST:     GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAG                         AATATTGTCCTTATCAGAGATCCAGAGGACTTCACAAAATTCTATCCC
genomic: GGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCC

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: 46 (upstream exon), 48 (downstream exon)
Score: 151

AGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCGTTCAACCTGGAAGACACATCAAGTTTTAGGGACCTTGATGAACACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 294

AGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCGTTCAACCTGGAAGACACATCAAGTTTTAGGGACCTTGATGAACACAG


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 44

AGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCGTTCAACCTGGAAGACACATCAAGTTTTAGGGACCTTGATGAACACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 590

AGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggt ... tgttctgcagAATATTGTCCTTATCAGAGATCCAGAGGACTCCACAAAATTCTATCCCCGTTCAACCTGGAAGACACATCAAGTTTTAGGGACCTTGATGAACACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAAAAAGATTATTGTAAAGATTAAAACAAGTGCTGAAAAGTCACTGTGGGTAGAGAAAGAGGACAATATCCGCCGTGGCCTTTTCGATTTACTACAGgtaattgggtcttctattttgatttaatttcattgttgctggcacactttattctccatgttatgacttctcctaagatatccagctcctttcctacttggtttaagtacagttgttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA