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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagctgataacaacactttgtttctcatgtccagtttcttagttacttagttcagtaatttacttcaaatgtgtgttgtgtgtgtttggtcagATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAAGCATGGGAAGAGAGTGAGAAGTCAAAGGCTGAGAACAG

Basic information

species Arabidopsis thaliana
transcript AT2G45820.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G45820.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g45070.1 (Oryza sativa), 3'ss of exon 2
gtcagctgataacaacactttgtttctcatgtccagtttcttagttacttagttcagtaatttacttcaaatgtgtgttgtgtgtgtttggtcagATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAAGCATGGGAAGAGAGTGAGAAGTCAAAGGCTGAGAACAG
              |   ||   |  |      ||  |||||  |  ||  ||   |||| | |   |||        |    ||       |||||||    |||||     ||||||  |||||||  |  ||||| |||||||||||||| || | ||||||| |||| |||||||||| 
-----------gtgattattaaataatttgagacatcttctttttgtctgggt---gtaact-ataccaataacaacgtaaaagttgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA
















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|86066947|gb|DR362704.1|DR362704
EST:     ATCGAGGAGCATACACCTAAGAAAGCTTCATCTGGTTCGGCCGGATAGAG                         ATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAA
genomic: ATCGAGGAGCATACACCTAAGAAAGCTTCATCTGGTTCGGCCG-ATAGAGgtcagctgat ... gtttggtcagATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAA
EST: gi|86060966|gb|DR356723.1|DR356723
EST:     CATCGAGGAGCATACACCTAAGAAAGCTTCATCTGGTTCGGCCGATAGAG                         ATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAAG
genomic: CATCGAGGAGCATACACCTAAGAAAGCTTCATCTGGTTCGGCCGATAGAGgtcagctgat ... gtttggtcagATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAAG
EST: gi|124864932|gb|EH949369.1|EH949369
EST:     TACACCTAAGAAAGCTTCATCTGGTTCGGCCGATAGAG                         ATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAAG
genomic: TACACCTAAGAAAGCTTCATCTGGTTCGGCCGATAGAGgtcagctgat ... gtttggtcagATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAAG
EST: gi|124738141|gb|EH829543.1|EH829543
EST:     TCGAGGAGCATACACCTAAGAAAGCTTCATCTGGTTCGGCCGATAGAG                         ATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCACTCATCAAAG
genomic: TCGAGGAGCATACACCTAAGAAAGCTTCATCTGGTTCGGCCGATAGAGgtcagctgat ... gtttggtcagATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAAG
EST: gi|124789305|gb|EH878984.1|EH878984
EST:     AGCATACACCTAAGAAAGCTTCATCTGGTTCGGCCGATAGAG                         ATGTGATACTTGCCGACTT
genomic: AGCATACACCTAAGAAAGCTTCATCTGGTTCGGCCGATAGAGgtcagctgat ... gtttggtcagATGTGATACTTGCCGACTT
EST: gi|163982673|gb|ES088401.1|ES088401
EST:     CGGCCGATAGAG                         ATGTGATACTTGCCGACTTGGAAAAAGAGAGGAAAACGTCATTCATCAAAG
genomic: CGGCCGATAGAGgtcagctgat ... gtttggtcagATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAAG
EST: gi|124707398|gb|EH798800.1|EH798800
EST:     CATCGAGGAGCATACACCTAAGAAAGCTTCATCTGGTTCGGCCGATAGAG                         ATGTGATACTTGCCGACTTGG
genomic: CATCGAGGAGCATACACCTAAGAAAGCTTCATCTGGTTCGGCCGATAGAGgtcagctgat ... gtttggtcagATGTGATACTTGCCGACTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttacttagttcagtaatttacttcaaatgtgtgttgtgtgtgtttggtcagATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAAGCATGGGAAGAGAGTGAGAAGTCAAAGGCTGAGAACAG
                 taatttacttcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagctgataacaacactttgtttctcatgtccagtttcttagttacttagttcagtaatttacttcaaatgtgtgttgtgtgtgtttggtcagATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAAGCATGGGAAGAGAGTGAGAAGTCAAAGGCTGAGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT