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

gtctgtcacattatatggccctttctcttttctatgtttgtgtctgaagatggctatgttttagaatttaaagaaatggataaatggattgtttttttcagAGACTTCCTCCGTTATCAACAGAACCAGACCGGTGTGAAAAAGCATTTGTTGGTAACACGATAGGTCAAGCAAATGGTGTCTATGACAAACCACTGGATC

Basic information

species Arabidopsis thaliana
transcript AT5G53490.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G53490.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G13640.1 (Glycine max), 3'ss of exon 2
-----gtctgtcacattatatggccctttctcttttctatgtttgtgtctgaagatggctatgttttagaatttaaagaaatggataaatggattgtttttttcagAGACTTCCTCCGTTATCAACAGAACCAGACCGGTGTGAAAAAGCATTTGTTGGTAACACGATAGGTCAAGCAAATGGTGTCTATGACAAACCACTGGATC
        | | |  || |      |    | |  | ||    ||| |   ||    ||  |   | || |   || | ||   |   |     | ||  || ||||| ||||| || || ||||| || ||  | || |||||    ||||||||||| ||||| || ||||| ||||||||||| ||||| |||||| | ||||
agcaaaagtttaaatttgtgaaagacaaa-tgtgatttacacatgtcttcaaaagaagcagt---tgaggagagaatgcaac--acccactatgttttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTTGGCAACACAATTGGTCAGGCAAATGGTGTATATGATAAACCATTAGATC

upper sequence: AT5G53490.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0098g01540.t01 (Vitis vinifera), 3'ss of exon 2
gtctgtcacattatatg-gccctttct--cttttctatgtttgtgtctgaagatggctatgttttagaatttaaagaaatggataaatggattgtttttttcagAGACTTCCTCCGTTATCAACAGAACCAGACCGGTGTGAAAAAGCATTTGTTGGTAACACGATAGGTCAAGCAAATGGTGTCTATGACAAACCACTGGATC
 | | |    | ||    |  ||||||  ||  | ||| | |||  |||  | ||   |||    |  || |  | | ||    |  | |  |  | ||| ||||| || ||||| || || ||||||||  |||| |||||    ||||||||||| |||||||| |||||||||||||| || |||||||| ||| | || |
ttttcttcagtcatccatgttctttctaactaatttatttctgttactgctgctgctgatg----atgatgtctatatattatgatgttgtcttatgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTTGGAAACACGATCGGTCAAGCAAATGGCGTTTATGACAAGCCAATCGACC
















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|125261147|gb|EL275232.1|EL275232
EST:     CTGCTAACCAG                         AGACTTCCTCCGTTATCAACAGAACCAGACCGGTGTGAAAAAGCATTTGTT
genomic: CTGCTAACCAGgtctgtcaca ... tttttttcagAGACTTCCTCCGTTATCAACAGAACCAGACCGGTGTGAAAAAGCATTTGTT
EST: gi|124772943|gb|EH863072.1|EH863072
EST:     TCTGTGCTTGCACTCTTACAATAGCTTCTCCTGTTATTGCTGCTAACCAG                         AGACTTCCTCCGT
genomic: TCTGTGCTTGCACTCTTACAATAGCTTCTCCTGTTATTGCTGCTAACCAGgtctgtcaca ... tttttttcagAGACTTCCTCCGT
EST: gi|125184887|gb|EL199841.1|EL199841
EST:     CTGC-AACCAG                         AGACTTCCTCCGTTATCAACAGAACCAGACCGGTGTGAAAAAGCATTTGTT
genomic: CTGCTAACCAGgtctgtcaca ... tttttttcagAGACTTCCTCCGTTATCAACAGAACCAGACCGGTGTGAAAAAGCATTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatggctatgttttagaatttaaagaaatggataaatggattgtttttttcagAGACTTCCTCCGTTATCAACAGAACCAGACCGGTGTGAAAAAGCATTTGTTGGTAACACGATAGGTCAAGCAAATGGTGTCTATGACAAACCACTGGATC
                                          ttgtttttttc  CT-rich tract
            ttttagaatttaaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtcacattatatggccctttctcttttctatgtttgtgtctgaagatggctatgttttagaatttaaagaaatggataaatggattgtttttttcagAGACTTCCTCCGTTATCAACAGAACCAGACCGGTGTGAAAAAGCATTTGTTGGTAACACGATAGGTCAAGCAAATGGTGTCTATGACAAACCACTGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA