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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagacacaaaaactttcccttttgttttgagtactactctgcttctttacttagcttttctcaaagcttttttttaatgaaattgcagAACGTGAAAGGAGTATTTGATGCAGCGATCCGAGTGGTTCTTCAACCTCCAAAGCAGAAGAAAAAGAAAAGCAAAGCACAAAAAGCCTGCTCCATTTTGT

Basic information

species Arabidopsis thaliana
transcript AT2G17800.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 6
gcaagacacaaaaactttcccttttgttttgagtactactctgcttctttacttagcttttctcaaagcttttttttaatgaaattgcagAACGTGAAAGGAGTATTTGATGCAGCGATCCGAGTGGTTCTTCAACCTCCAAAGCAGAAGAAAAAGAAAAGCAAAGCACAAAAAGCCTGCTCCATTTTGT
     | | ||     |    ||||  |||   |||      | |   ||| || | |  ||  |||  | | ||| |     ||||||||||||||| | ||||||||||||||| ||  |||| || |||||||| |||||||| ||||||||||| || ||||||||||| || || || || ||||
---gtatataattgaatgaattttttcttttcatacccaatggttaagttaattgg-tagtcataaatttatctttgacctttattgcagAACGTGAAGGCAGTATTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCAAAGCAAAAGAAAAAGAAGAGTAAAGCACAAAAGGCATGTTCAATATTGT

upper sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 7
----gcaagacacaaaaactttcccttttgttt-tgagtac--tactctgcttct---ttacttagcttttctcaaagcttttttttaatgaaattgcagAACGTGAAAGGAGTATTTGATGCAGCGATCCGAGTGGTTCTTCAACCTCCAAAGCAGAAGAAAAAGAAAAGCAAAGCACAAAAAGCCTGCTCCATTTTGT
     |||      | | || |  |  ||||   ||| | |  || |  || | |     ||   ||  |  ||  |    ||  |   |   ||||||||| ||||||| ||| ||||||||||| |||   ||||||||||| || || ||||||||||| |||||||  ||| || || ||   ||    | | || 
ggtcacaacgtgtcatagctctagcaattgtagatgattccggtaattggcgtttaaacaacaccgccatcttctgatgcgttgctgtctttcattgcagAATGTGAAAGCAGTTTTTGATGCAGCAATCAAGGTGGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAAAA-AAAACAAAAGAACTGTGTCATACTCTGA
















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|125133860|gb|EL175103.1|EL175103
EST:     GCTCCCGCATACATCGAGTGCAGTTCAAAAACACAAGAG                         AACGTGAAAGGAGTATTTGATGCAGCGATCCGAGTGGTTCTTCAACCTCC
genomic: GCTCCCGCATACATCGAGTGCAGTTCAAAAACACAAGAGgcaagacaca ... gaaattgcagAACGTGAAAGGAGTATTTGATGCAGCGATCCGAGTGGTTCTTCAACCTCC
EST: gi|124928694|gb|EL006317.1|EL006317
EST:     AACTAATTGGAGCTCCCGCATACATCGAGTGCAGTTCAAAAACACAAGAG                         AACGTGAAAGGA
genomic: AACTAATTGGAGCTCCCGCATACATCGAGTGCAGTTCAAAAACACAAGAGgcaagacaca ... gaaattgcagAACGTGAAAGGA
EST: gi|125051742|gb|EL123831.1|EL123831
EST:     AACTAATTGGAGCTCCCGCATACATCGAGTGCAGTTCAAAAACACAAGAG                         AACGTGAAAGGA
genomic: AACTAATTGGAGCTCCCGCATACATCGAGTGCAGTTCAAAAACACAAGAGgcaagacaca ... gaaattgcagAACGTGAAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactctgcttctttacttagcttttctcaaagcttttttttaatgaaattgcagAACGTGAAAGGAGTATTTGATGCAGCGATCCGAGTGGTTCTTCAACCTCCAAAGCAGAAGAAAAAGAAAAGCAAAGCACAAAAAGCCTGCTCCATTTTGT
                                      ttttaat  putative branch site (score: 3)
                             aaagcttttttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagacacaaaaactttcccttttgttttgagtactactctgcttctttacttagcttttctcaaagcttttttttaatgaaattgcagAACGTGAAAGGAGTATTTGATGCAGCGATCCGAGTGGTTCTTCAACCTCCAAAGCAGAAGAAAAAGAAAAGCAAAGCACAAAAAGCCTGCTCCATTTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG