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'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgttagtgagagagaacaatcatgttatggtgtagaagggtttcgtttggcatattagatatatctcagtatctgctgagtaactcctatttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT

Basic information

species Zea mays
transcript GRMZM2G104377_T03
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104377_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os05g01060.1 (Oryza sativa), 3'ss of exon 16
tatgttagtgaga-gagaacaatcatgttatggt-gtagaaggg--tttcgtttggcatattagatatatctcagtatctgctgagtaactcctatttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT
 ||   |   | |  |  || ||| |  ||  |  || |||||   |||| ||||| |||||   | ||  | | |||    ||| |||     |||| |||||| |||||||| |||||||  || ||||||||||| ||  | |||||||| || |||||||||||  | |||
catagcaacaaaacaaccaccatcctaatagagaagtggaaggtattttcttttggtatatt---tctaatt-aatattacatgaataatcatcatttatgcagATCCTGAAACAAAGGAGCTCATCAAGAAAATTCTTTCAATTGGGCATGTATCCTATGAAGTTCTGCTGCCT
















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|78021163|gb|DV489550.1|DV489550
EST:     GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTG                         ACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
genomic: GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTGgtgagttcct ... atttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
EST: gi|5714191|gb|AI944176.1|AI944176
EST:     GGGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTG                         CCCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
genomic: GGGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTGgtgagttcct ... atttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
EST: gi|5296168|gb|AI783043.1|AI783043
EST:     GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTG                         ACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
genomic: GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTGgtgagttcct ... atttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
EST: gi|60351693|gb|DN218666.1|DN218666
EST:     GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTG                         ACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
genomic: GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTGgtgagttcct ... atttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
EST: gi|211204845|gb|FL182852.1|FL182852
EST:     GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTG                         ACCCTGAAACCAAGGAGCATATTAAGAAAATTCTC
genomic: GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTGgtgagttcct ... atttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTC
EST: gi|19058452|gb|BM737119.1|BM737119
EST:     GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTG                         ACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
genomic: GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTGgtgagttcct ... atttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
EST: gi|60355764|gb|DN222737.1|DN222737
EST:     GGGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTG                         ACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
genomic: GGGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTGgtgagttcct ... atttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
EST: gi|31353499|gb|CD437856.1|CD437856
EST:     GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTG                         ACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT
genomic: GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTGgtgagttcct ... atttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCT

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), 47 (downstream exon)
Score: 215

GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTGgtgagttcct ... atttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 73

GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTGgtgagttcct ... atttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 102

GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTGgtgagttcct ... atttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 143

GGCGAGATTGTGAAGGTTTATGCTAATGATCAAAGAAAAATTACATGTGgtgagttcct ... atttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtttggcatattagatatatctcagtatctgctgagtaactcctatttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT
                                  gagtaac  putative branch site (score: 143)
                                        ctcctattt  CT-rich tract
        atattagatatatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgttagtgagagagaacaatcatgttatggtgtagaagggtttcgtttggcatattagatatatctcagtatctgctgagtaactcctatttgtgcagACCCTGAAACCAAGGAGCATATTAAGAAAATTCTCTCTCTGGGGCATGTCTCTTATGAAGTTCTATTACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - -gaacaat
- - - - - - - - - - - catgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgctg