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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatctcatttctaattttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG

Basic information

species Arabidopsis thaliana
transcript AT2G47510.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 8
gtatatctcatttctaattttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
       |   || ||   ||| ||  | ||     |   |  | |||   |  ||  |  |  |||   ||  |     || |  |      |||  | | |      | | ||| |||||||  || |||||||||||||| ||||| ||||||||| | || ||||| || ||||| ||||||||||||||| ||
-------ttggtt-taggattactttga-aacagagtgttaattccatgctt--tacctaaggcgttcctttcat-----ttatttaaatacctaaatccaatctgtctttttcagATTTGATGCCAAAATAGCTGCTGCAGTGGCTGAGGAAACAAACCTACCCTTTGTGACAGCAGAGAACAAGTTTGAAGCTTTG

upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 8
gtatatctcatttctaatt--ttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
       | |||   || |  | | | ||| |  | | |   | |     ||     |||| ||  |||| | ||  |       |  || ||  |||   |    ||     | |||||||||||  |||||||| || ||||||||||| ||||||||  |||| |||||||| |||||||| |||||||| ||  ||
-------ttattatgaaataataaataccaaacctaccttttaagg----ctgaagaaaatatgtggtttaactaaaga------taaacagtgataattttctagatgaa-attcagGTTTGATGCCAAGATAGCAGCAGCAGTAGCTGAGGAAACAAATCTGCCTTTTGTCACGGCAGAAAATAAGTTTGAGGCCTTG

upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 8
gtatatctcatttctaattttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
  | |      |  |  |||  | | |  ||    ||    |||| | ||     | |  | |  ||  || |       |  |   ||| |  ||               | |||||||||||  |||||||| || ||||||||||| ||||||||  |||| ||||| || |||||||| |||||||| ||  ||
--acaagcttgtagtggtttattatgctgaagaaaatatgtggtttaacttctaaagaaataaatttggataaacaatgataatttcctggatgaa--------------attcagGTTTGATGCCAAGATAGCAGCAGCAGTAGCTGAGGAAACAAATCTGCCTTTTGTTACGGCAGAAAATAAGTTTGAGGCCTTG

upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 8
gtatatctcatttctaattttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
 ||   |    || |||||||||    |  |    ||     ||| | || |   | |  | |  ||  || |       |  |   ||| | ||| | |             |||||||||||  || ||||| || ||||||||||| ||||| ||  |||| ||||| || |||||||| |||||||| ||  ||
ttactacaagcttgtaattttatgctgaagaaaatatgtt--gtttaacttttaaagaaataaatttggataaacaatgataatttcctgga-taaaatt-------------cagGTTTGATGCCAAAATAGCAGCAGCAGTAGCTGAGGAAACCAATCTGCCTTTTGTTACGGCAGAAAATAAGTTTGAGGCCTTG

upper sequence: AT2G47510.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 9
-gtatatctcatttctaattttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
 |||| |      | ||||||| | || ||  |   ||   | || ||| | ||| | ||| | ||||||          || || ||   |||| | | |  | |  |   |  |||||||||||||||||||||   ||||| || || |||||||| || ||||| ||||| |||||||||||||||||||| |||
agtatgt---gcatttaattttctctcaatcttattat--gaagtccatttatcc-atattagttgtttt----------ttagttcatgatagtca-atttttgagcttcatttagGTTTGATGTAAAGATAGCTAGAGCAGTTGCCGAGGAAACAAATTTACCATTCGTCACAGCAGAAAACAAGTTTGAAGCACTG

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|116480251|gb|EG522843.1|EG522843
EST:     CTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG                         GTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
genomic: CTTGCACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGGgtatatctca ... atctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
EST: gi|164069209|gb|ES171603.1|ES171603
EST:     TTGACACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGG                         GTTTGATGTAAAGATAGCTGC
genomic: TTG-CACAAGGTGGAACTGCGGTTGGGACAGGATTAAACACTAAGAAAGGgtatatctca ... atctgtacagGTTTGATGTAAAGATAGCTGC
EST: gi|125013157|gb|EL085426.1|EL085426
EST:     GGACAGGATTAAACACTAAGAAAGG                         GTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT
genomic: GGACAGGATTAAACACTAAGAAAGGgtatatctca ... atctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG
                             tagtaac  putative branch site (score: 1)
     tttattagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatctcatttctaattttatttccataattccatcccaggttcatctctcctaaatttgatgttttattagtgggctttgtccactgtagtaacactagtaatatctgtacagGTTTGATGTAAAGATAGCTGCTGCAGTAGCTGAAGAAACAAACTTGCCATTTGTCACTGCAGAAAACAAGTTTGAAGCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC