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'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagaaccccctacatagtgagggaaatgcaagcttcaaaacaaatacatgtacataggtcactccattcaattctaagcattgaagaatctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCTGCTTACCGAAAGGCAAAGTCATTGAAGGCGGCTAGCAAACGGGGTCCTG

Basic information

species Zea mays
transcript GRMZM5G804064_T01
intron # 17
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|47962731|gb|CN845440.1|CN845440
EST:     CCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAG                         GAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCT
genomic: CCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAGgttcggttct ... tctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCT
EST: gi|37391010|gb|CF632744.1|CF632744
EST:     CCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAG                         GAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCT
genomic: CCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAGgttcggttct ... tctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCT
EST: gi|21390142|gb|BQ528191.1|BQ528191
EST:     CCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAG                         GAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCT
genomic: CCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAGgttcggttct ... tctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCT
EST: gi|26457191|gb|CA828774.1|CA828774
EST:     CCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAG                         GAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCT
genomic: CCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAGgttcggttct ... tctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCT
EST: gi|45568255|gb|CK985977.1|CK985977
EST:     CCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAG                         GAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCT
genomic: CCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAGgttcggttct ... tctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCT
EST: gi|13149411|gb|BG319733.1|BG319733
EST:     CCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAG                         GAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCT
genomic: CCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAGgttcggttct ... tctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCT

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: 95

AAGGACCTACCAAGGAAGAAACGCCGAAGATTAGAGGCCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAGgttcggttct ... tctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCTGCTTACCGAAAGGCAAAGTCATTGAAGGCGGCTAGCAAACGGGGTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

AAGGACCTACCAAGGAAGAAACGCCGAAGATTAGAGGCCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAGgttcggttct ... tctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCTGCTTACCGAAAGGCAAAGTCATTGAAGGCGGCTAGCAAACGGGGTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

AAGGACCTACCAAGGAAGAAACGCCGAAGATTAGAGGCCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAGgttcggttct ... tctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCTGCTTACCGAAAGGCAAAGTCATTGAAGGCGGCTAGCAAACGGGGTCCTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 40

AAGGACCTACCAAGGAAGAAACGCCGAAGATTAGAGGCCCAGCGAGAGATGCTGGAAGATGAGGATGAAGATGACGAGGAAGCAAAGgttcggttct ... tctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCTGCTTACCGAAAGGCAAAGTCATTGAAGGCGGCTAGCAAACGGGGTCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacatgtacataggtcactccattcaattctaagcattgaagaatctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCTGCTTACCGAAAGGCAAAGTCATTGAAGGCGGCTAGCAAACGGGGTCCTG
                                           aatctatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagaaccccctacatagtgagggaaatgcaagcttcaaaacaaatacatgtacataggtcactccattcaattctaagcattgaagaatctattacagGAAAGTGATAGAGGGAAGAAACTGAAGAAAGGCCAGTCTCTAGTGGATGCTGCTTACCGAAAGGCAAAGTCATTGAAGGCGGCTAGCAAACGGGGTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - -ccctaca
- - - - - - - - - - - - - - tgcaagc
- - - - - - - - - - - - - - - - - - - aaaacaa
- - - - - - - - - - - - - - - - - - - - - - -atacatg