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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgccatttatttttgcctggtagtctatatgtttctttgagacctttggttgtatacaacacatgaatatcttagttgtactttttgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAG

Basic information

species Zea mays
transcript GRMZM2G416120_T01
intron # 6
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|50328354|gb|CO523480.1|CO523480
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
EST: gi|71425566|gb|DR806758.1|DR806758
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
EST: gi|149073906|gb|EE162234.2|EE162234
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCCAT-GATCTTAATTCATGACAAGAAAGTGACAAATAT
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCC-ATTGATCTTAATTCATGACAAGAAAGTGACAAATAT
EST: gi|78078492|gb|DV506905.1|DV506905
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
EST: gi|67019174|gb|CO447923.1|CO447923
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
EST: gi|149077207|gb|EE165873.2|EE165873
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCATTGATCTT
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTT
EST: gi|71425565|gb|DR806757.1|DR806757
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGT                         GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATG

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: 653

CAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

CAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

CAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 431

CAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGAAATGTgtaagtgcca ... tgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacctttggttgtatacaacacatgaatatcttagttgtactttttgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAG
                                      tacttttt  CT-rich tract
                         aatatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgccatttatttttgcctggtagtctatatgtttctttgagacctttggttgtatacaacacatgaatatcttagttgtactttttgtatcgcagGAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG