Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTATGGTAGTCAGGGATATGGTGCTAAAAGATCAACTGATAGTTTCAAGAACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattggtttctgtttgaatgcttccttttagcctagtacaacactaacgagtcatcaattagcag

Basic information

species Zea mays
transcript GRMZM2G066440_T01
intron # 9
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|211094279|gb|FL470654.1|FL470654
EST:     AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|111991228|gb|EE332430.1|EE332430
EST:     GTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: GTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|16919952|gb|BM074437.1|BM074437
EST:     AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|24764480|gb|CA399644.1|CA399644
EST:     AACAGCAGCTTCGGCAACCAGGCCGGTGGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCCAGTGGCAATCAGTTCGGTGGTACTACCAGCTTTCA
genomic: AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|32907008|gb|CF011821.1|CF011821
EST:     GGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: GGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|50336102|gb|CO531228.1|CO531228
EST:     AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|32919364|gb|CF024176.1|CF024176
EST:     GGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: GGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|37401565|gb|CF638149.1|CF638149
EST:     AACAGCAGCTTCGGCAACCAGGCCGGTGGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCCAGTGGCAATCAGTTCGGTGGTACTACCAGCTTTCA
genomic: AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|60341740|gb|DN208713.1|DN208713
EST:     AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|116823588|gb|EC867128.1|EC867128
EST:     GGTGGTTCATGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: GGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|33095213|gb|CF055207.1|CF055207
EST:     AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|149072974|gb|EE161235.2|EE161235
EST:     AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|50336101|gb|CO531227.1|CO531227
EST:     CGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: CGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|32921823|gb|CF026635.1|CF026635
EST:     AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
EST: gi|78120607|gb|DV538991.1|DV538991
EST:     AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAG                         CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA
genomic: AACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 617

CTTATGGTAGTCAGGGATATGGTGCTAAAAGATCAACTGATAGTTTCAAGAACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 304

CTTATGGTAGTCAGGGATATGGTGCTAAAAGATCAACTGATAGTTTCAAGAACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 332

CTTATGGTAGTCAGGGATATGGTGCTAAAAGATCAACTGATAGTTTCAAGAACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 388

CTTATGGTAGTCAGGGATATGGTGCTAAAAGATCAACTGATAGTTTCAAGAACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattg ... caattagcagCTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTATGGTAGTCAGGGATATGGTGCTAAAAGATCAACTGATAGTTTCAAGAACAGCAGCTTCGGCAACCAGGCCGGGGGTGGTTCAAGCTTTCACTCGAGgtatgtattggtttctgtttgaatgcttccttttagcctagtacaacactaacgagtcatcaattagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT