Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcttcttcactgattttactgaatgcaagtttaatcactggagaactggctatgtttgtttctgaattagtctgcaaattaggattaattgggtaggtttgattgcagAGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCAAAGGATGAAGTTCAAATCTACACTTGGAAAGATGCCAGTCTTCGCGAGC

Basic information

species Arabidopsis thaliana
transcript AT2G45640.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G45640.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G060669_T04 (Zea mays), 3'ss of exon 3
gtactcttcttcactgattttactgaatgcaagtttaatcactggagaactggctatgtttgtttctgaattagtctgcaaattaggattaattgggtaggtttgattgcagAGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCAAAGGATGAAGTTCAAATCTACACTTGGAAAGATGCCAGTCTTCGCGAGC
 |||   | ||     || |||     | || || |   || | ||||  ||   |          || | |   | | || ||     | ||  | ||    || || |||  || |||||| ||    | |||||| | | |||||||||| ||||||||||||||||||||||| || ||||| ||||| ||||||| ||| || ||||
ctacatatattgtggcatcttatct--tacatgtcttg-cagtagaga-ttgataagaaaacaccatgtactg--cagaaagttga---tcatcagtta---ctgttttcagGTTGCTGGTCACCACCAAAATGAAGAGTTTTCTGTGAGAGGGAAAGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCCACTCTCCGTGAGC

upper sequence: AT2G45640.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G064988_T03 (Zea mays), 3'ss of exon 2
gtactcttcttcactgattttactgaatgcaagtttaatcactggagaactggctatgtttgtttctgaattagtctgcaaattaggattaattgggtaggtttgattgcagAGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCAAAGGATGAAGTTCAAATCTACACTTGGAAAGATGCCAGTCTTCGCGAGC
    | |  |   |  || ||      | || |  |     | | |||  | | || |        || |  | |   |  |  |   || |  |  |     || || |||  || |||||| ||    | |||||| | ||| |||||||| || |||||||||||||||||||| || ||||| ||||| ||||| |  || |||||||
----tatattgtgcacatcttgtct--tacatgcct---tgcagtagagattgataagaca--ccatggacca-tgcactgaagaaagttgaccgtttgttactgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCGACCCTCCGCGAGC
















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|116483742|gb|EG526334.1|EG526334
EST:     ACATGTCCCCTTCTTCTTCGTGTTTTCACCAAG                         AGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCA
genomic: ACATGTCCCCTTCTTCTTCGTGTTTTCACCAAGgtactcttct ... ttgattgcagAGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCA
EST: gi|152038382|gb|AV821346.2|AV821346
EST:     ACATGTCCCCTTCTTCTTCGTGTTTTCACCAAG                         AGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCA
genomic: ACATGTCCCCTTCTTCTTCGTGTTTTCACCAAGgtactcttct ... ttgattgcagAGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCA
EST: gi|86075848|gb|DR371605.1|DR371605
EST:     ACATGTCCCCTTCTTCTTCGTGTTTTCACCAAG                         AGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAAGCAAAGAACCA
genomic: ACATGTCCCCTTCTTCTTCGTGTTTTCACCAAGgtactcttct ... ttgattgcagAGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCA
EST: gi|124754983|gb|EH845113.1|EH845113
EST:     ACATGTCCCCTTCTTCTTCGTGTTTTCACCAAG                         AGTGGTGGTCAT
genomic: ACATGTCCCCTTCTTCTTCGTGTTTTCACCAAGgtactcttct ... ttgattgcagAGTGGTGGTCAT
EST: gi|152033713|gb|BP562681.3|BP562681
EST:     ACATGTCCCCTTCTTCTTCGTGTTTTCACCAAG                         AGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCA
genomic: ACATGTCCCCTTCTTCTTCGTGTTTTCACCAAGgtactcttct ... ttgattgcagAGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgtttctgaattagtctgcaaattaggattaattgggtaggtttgattgcagAGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCAAAGGATGAAGTTCAAATCTACACTTGGAAAGATGCCAGTCTTCGCGAGC
                      aaattaggattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcttcttcactgattttactgaatgcaagtttaatcactggagaactggctatgtttgtttctgaattagtctgcaaattaggattaattgggtaggtttgattgcagAGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCAAAGGATGAAGTTCAAATCTACACTTGGAAAGATGCCAGTCTTCGCGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG