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'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatttcccagcctcagccactgggtctctgtcaaatgcttgagattaatgcagtgtttcacatgctatttttttgttctcttttgtggctatgaacagCAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAG

Basic information

species Zea mays
transcript GRMZM2G009849_T02
intron # 31
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 31
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 48
--atcatttcccagcctcagccactgggtctctgtcaaat----gcttg-agattaatgcagtgtttcacatgctatttttttgttctcttttgtggctatgaacagCAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAG
  |  ||| |  |  || | | |      |  |   ||||    ||||| | |||  | |||   || |  | ||||||| |  |||| ||    |  ||||   ||||||||||||||||||| ||||||||||| || ||||| ||||||||||| |||||  | || ||||| || |||||||| || || ||||| |||
gtagtattactgattcttaactaacataacatttgtaaattactgcttgcaaatttgtacagcaattgatgttctattttgtctttctttt----gattatgggtagCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 31
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 20
------------------------------------------------------------------atcatttcccagcctcagccactgggtctctgtcaaatgcttgagattaatgcagtgtttcacatgctatttttttgttctcttttgtggctatgaacagCAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAG
                                                                   | || |       |||    ||       |||   ||  |  |  | | |      | |  | ||  | |  ||   |   |||| |  | |    ||||| || ||||||||| | ||||||||||| || |||||||||||||| |||||||| || || ||||| || || || ||||| || ||||| |||
gtactataatgtttttattttcttcatttattgttttgaagatcatatttgaggttgttcatgggtgttatgttttgctttcaatttctttagtggtgt-gtatattcaatctcattttctcctgttgcttgacaatgattctcttgtttttatttcaacttgcagCAGGAACTTGCTGCTATATTCAAGAAAATTGGTGACAAGCAAACATGCACTATTGGTTTATATGAACTATACCGTATTACTCAACTGTACCCCAAG
















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|18450668|gb|BM428946.1|BM428946
EST:     CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTGTCTTCA
genomic: CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAGgtccgactgt ... ctatgaacagCAAGAGCTTGCTGCTGTCTTCA
EST: gi|67019308|gb|CO448057.1|CO448057
EST:     CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACT
genomic: CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAGgtccgactgt ... ctatgaacagCAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACT
EST: gi|12045716|gb|BF727855.1|BF727855
EST:     CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACT
genomic: CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAGgtccgactgt ... ctatgaacagCAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACT
EST: gi|67011174|gb|CO439923.1|CO439923
EST:     CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACT
genomic: CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAGgtccgactgt ... ctatgaacagCAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACT
EST: gi|87152573|gb|DY397362.1|DY397362
EST:     CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTGTCTTCAAG
genomic: CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAGgtccgactgt ... ctatgaacagCAAGAGCTTGCTGCTGTCTTCAAG
EST: gi|32851907|gb|CD991588.1|CD991588
EST:     CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACT
genomic: CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAGgtccgactgt ... ctatgaacagCAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACT
EST: gi|19822797|gb|BQ048821.1|BQ048821
EST:     CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAG                         CAAGAGCTTGCTGCTGTCTT
genomic: CTTCAAACAATCCAAATCCATCTACTCACTCAGCAGACGCGCAATTGAAGgtccgactgt ... ctatgaacagCAAGAGCTTGCTGCTGTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaatgcagtgtttcacatgctatttttttgttctcttttgtggctatgaacagCAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAG
 gattaat  putative branch site (score: 3)
                      tatttttttgttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcatttcccagcctcagccactgggtctctgtcaaatgcttgagattaatgcagtgtttcacatgctatttttttgttctcttttgtggctatgaacagCAAGAGCTTGCTGCTGTCTTCAAGAAAATCGGCGACAAGCAAACATGTACTATTGGCTTCTACGAACTGTATCGGATAACTCAGCTCTACCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC