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'   		20  
 5'  3'   
21  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttattgagtagctgttctgtctcttattttattcagtcatgtccattaggctggtactaaactaataaagttcaacaatgcaataattgctgatacaatcattttacttgtattgctatctactgttgccttgtataactgttgaattttgatttaataaattttgggtgctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGTGACATGCGGTGTTGGGATGCCCCTGAAAAGGCAGATATTTTG

Basic information

species Zea mays
transcript GRMZM2G011456_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011456_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g04660.2 (Oryza sativa), 3'ss of exon 9
gtaagttattgagtagctgttctgtctcttattttattcagtcatgtccattaggctggtactaaactaataaagttcaacaatgcaataattgctgatacaatcattttacttgtattgctatctactgttgccttgtataactgttgaattttgatttaataaattttggg-tgctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGTGACATGCGGTGTTGGGATGCCCCTGAAAAGGCAGATATTTTG
                                                                                      |    ||| |||||      |||| ||  | ||  |       ||   |   ||| | |     ||    || | ||    ||||||  | ||||||||||||||||||||||||| || ||||||||| |||||||| ||||||| |||||||||||||| ||||| |||||||| || ||||||||||||
-------------------------------------------------------------------------------------tatgttttgttgatagtcgggtttttctcctgtttatcctgtacgtgtgcaaatatgattacatgatgactatctgatgtgctttggggcggtgaaacagAGTTTGATCAAATTGGAAGGATGGGAAAGCTTGGTTACTATAATTTCAAGTGACATGCGGTGCTGGGAAGCCCCTGAGAAAGCAGATATTTTG
















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|20803221|gb|BQ294271.1|BQ294271
EST:     TCCTAACGCTGTTATTACTCTTCAT                         AGTTTGATCAAATTGGAGGGTTGTTTAAAGCCTGGTTACTGTAATTTCTAG
genomic: TCCTAACGCTGTTATTACTCTTCATgtaagttatt ... gctgaaacagAGTTTGATCAAATTGGAGGGTTG-GGAAAGCCTGGTTACTGTAATTTCTAG
EST: gi|21843268|gb|BQ703849.1|BQ703849
EST:     TCCTAACGCTTTTATTACTCTTCAT                         AGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGT
genomic: TCCTAACGCTGTTATTACTCTTCATgtaagttatt ... gctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGT
EST: gi|211483571|gb|FL225316.1|FL225316
EST:     TAAAAGTATATGCTGTTGNNNNNNNTCCTAACGCTGTTATTACTCTTCAT                         AGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGT
genomic: TAAAAGTATATGCTGTTGAAAAAAATCCTAACGCTGTTATTACTCTTCATgtaagttatt ... gctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGT
EST: gi|60340216|gb|DN207189.1|DN207189
EST:     TAAAAGTATATGCTGTTGNNNNNNNTCCTAACGCTGTTATTACTCTTCAT                         AGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGT
genomic: TAAAAGTATATGCTGTTGAAAAAAATCCTAACGCTGTTATTACTCTTCATgtaagttatt ... gctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGT
EST: gi|26456816|gb|CA828399.1|CA828399
EST:     TAAAAGTATATGCTGTTGNNNNNNNTCCTAACGCTGTTATTACTCTTCAT                         AGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGT
genomic: TAAAAGTATATGCTGTTGAAAAAAATCCTAACGCTGTTATTACTCTTCATgtaagttatt ... gctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGT
EST: gi|12971842|gb|BG267685.1|BG267685
EST:     TAAAAGTATATGCTGTTGNNNNNNNTCCTAACGCTGTTATTACTCTTCAT                         AGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGG
genomic: TAAAAGTATATGCTGTTGAAAAAAATCCTAACGCTGTTATTACTCTTCATgtaagttatt ... gctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGG
EST: gi|26557923|gb|CA830158.1|CA830158
EST:     TCCTAACGCTGTTATTACTCTTCAT                         AGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGT
genomic: TCCTAACGCTGTTATTACTCTTCATgtaagttatt ... gctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGT
EST: gi|60397916|gb|DN230732.1|DN230732
EST:     TAAAAGTATATGCTGTTGNNNNNNNTCCTAACGCTGTTATTACTCTTCAT                         AGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGT
genomic: TAAAAGTATATGCTGTTGAAAAAAATCCTAACGCTGTTATTACTCTTCATgtaagttatt ... gctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGT

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), 48 (downstream exon)
Score: 129

GCTGCTGAAGAAACTGGTCGCAAGTTAAAAGTATATGCTGTTGAAAAAAATCCTAACGCTGTTATTACTCTTCATgtaagttatt ... gctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGTGACATGCGGTGTTGGGATGCCCCTGAAAAGGCAGATATTTTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 88

GCTGCTGAAGAAACTGGTCGCAAGTTAAAAGTATATGCTGTTGAAAAAAATCCTAACGCTGTTATTACTCTTCATgtaagttatt ... gctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGTGACATGCGGTGTTGGGATGCCCCTGAAAAGGCAGATATTTTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 54

GCTGCTGAAGAAACTGGTCGCAAGTTAAAAGTATATGCTGTTGAAAAAAATCCTAACGCTGTTATTACTCTTCATgtaagttatt ... gctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGTGACATGCGGTGTTGGGATGCCCCTGAAAAGGCAGATATTTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

GCTGCTGAAGAAACTGGTCGCAAGTTAAAAGTATATGCTGTTGAAAAAAATCCTAACGCTGTTATTACTCTTCATgtaagttatt ... gctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGTGACATGCGGTGTTGGGATGCCCCTGAAAAGGCAGATATTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgccttgtataactgttgaattttgatttaataaattttgggtgctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGTGACATGCGGTGTTGGGATGCCCCTGAAAAGGCAGATATTTTG
      ttgtataactgttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttattgagtagctgttctgtctcttattttattcagtcatgtccattaggctggtactaaactaataaagttcaacaatgcaataattgctgatacaatcattttacttgtattgctatctactgttgccttgtataactgttgaattttgatttaataaattttgggtgctgaaacagAGTTTGATCAAATTGGAGGGTTGGGAAAGCCTGGTTACTGTAATTTCTAGTGACATGCGGTGTTGGGATGCCCCTGAAAAGGCAGATATTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT