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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttctttcactttttacctgtcaaacactacatgtgctgatgctgtcccaaaattgtagtcttcacatttttcctcttttattgttatcttgtagATCTTGGGGTTTTCTTTGCCCTGTTCACACTCCTGATGGAACACCTTGTGGATTACTGAATCATATGACTCGTACTAGCC

Basic information

species Arabidopsis thaliana
transcript AT1G29940.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G29940.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G388892_T02 (Zea mays), 3'ss of exon 14
gtaggttctttcactttttacctgtcaaacactacatgtgctgatgctgtcccaaaattgtagtcttcacatttttcctcttttattgttatcttgtagATCTTGGGGTTTTCTTTGCCCTGTTCACACTCCTGATGGAACACCTTGTGGATTACTGAATCATATGACTCGTACTAGCC
                | |   | ||   | ||  ||||  |  ||||||       ||| |    |   |  |   | ||   | |||   |||||||||| |||||||| || || || ||||| || ||||| |||   |||||||| ||||||||||| ||||||  |||  |||
---------------gtatgtttatc---ctcttaatgtcattctgctgttgtttgcttgcatctattgtacctg--cactgaaaatgtc--cttgtagATCATGGGGTTTCCTGTGTCCAGTTCATACACCTGACGGAGAGCCTTGTGGTTTACTGAATCACATGACTTCTACATGCC

upper sequence: AT1G29940.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA17G23500.1 (Glycine max), 3'ss of exon 9
gtaggttctttcactttttacctgtcaaacactacatgtgctgatgctgtcccaaaattgtagtcttcacatttttcctcttttattgttatcttgtagATCTTGGGGTTTTCTTTGCCCTGTTCACACTCCTGATGGAACACCTTGTGGATTACTGAATCATATGACTCGTACTAGCC
          | | |  ||   |  || |  | |||  |  || |  |||   || ||  |  |   ||   ||||  | | | |           ||||||||||||||||||||||||||| ||||| |||||||||   || ||||||||  |||||||||||||| | |||||  
---------gttagtactttttta-catagtcgacagattgtgtttttgttataatatcct--tacgcatgatttttatatataa----------atagATCTTGGGGTTTTCTTTGCCCTGTGCACACACCTGATGGAGAGCCCTGTGGATTGTTGAATCATATGACTTGCACTAGTA

upper sequence: AT1G29940.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA13G26190.1 (Glycine max), 3'ss of exon 18
gtaggttctttcactttttacctgtcaaacactacatgtgctgatgctgtcccaaaattgtagtcttcacatttttcctcttttattgttatcttgtagATCTTGGGGTTTTCTTTGCCCTGTTCACACTCCTGATGGAACACCTTGTGGATTACTGAATCATATGACTCGTACTAGCC
              ||  ||| | | | |||  |   ||    |   |||       || || | | |  |  | |  | ||||||   |||    |||||||||||||||||| |||||||| ||||| |||||||||   || ||||||||  |||||||||||||| | |||||  
-------------gttagtactt-ttatacataatcggt----agattgtgattttgttataatatacttacctatgtttttttatatatataa-atagATCTTGGGGTTTTCTCTGCCCTGTGCACACACCTGATGGAGAGCCCTGTGGATTGTTGAATCATATGACTTGCACTAGTA

upper sequence: AT1G29940.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv13s0084g00600.t01 (Vitis vinifera), 3'ss of exon 14
gtaggttctttcactttttacctgtcaaacactacatgtgctgatgctgtcccaaaattgtagtcttcacatttttcctcttttattgttatcttgtagATCTTGGGGTTTTCTTTGCCCTGTTCACACTCCTGATGGAACACCTTGTGGATTACTGAATCATATGACTCGTACTAGCC
          |   | |||   ||  ||    |  |||| || |   ||    |  ||| |  |||| |   |||   ||| |||       |||  ||| |||||||||||||||||||||||||||| ||||||||    ||||||||||| ||||| |||||| ||  |||| | |
---------gtatgtatttgtttggaaagtttttaatgtacttagcttg----agtattatgatcttga---tttatttctctta-------cttccagAGCTTGGGGTTTTCTTTGCCCTGTTCACACACCTGATGGGGAGCCTTGTGGATTGCTGAACCATATGGCTTCTACTTGTC

upper sequence: AT1G29940.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: EFJ35146 (Selaginella moellendorffii), 3'ss of exon 15
gtaggttctttcactttttacctgtcaaacactacatgtgctgatgctgtcccaaaattgtagtcttcacatttttcctcttttattgttatcttgtagATCTTGGGGTTTTCTTTGCCCTGTTCACACTCCTGATGGAACACCTTGTGGATTACTGAATCATATGA-CTCGTACTAGCC
                                                     |  |   |  |  |       | ||| |    || |     |||||||| ||||| ||||||||||| ||||||||||| |||||   ||||||||| || || | |||| | | ||| |  |    
--------------------------------------------------gtaaggacactgattctactccagtccctttaactttatggatgtgtagATCGTGGGGATTTCTTTGCCCCGTTCACACTCCCGATGGTGAACCTTGTGGGTTGCTCACTCATTTAAGCTCATTGTGCA-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgtcccaaaattgtagtcttcacatttttcctcttttattgttatcttgtagATCTTGGGGTTTTCTTTGCCCTGTTCACACTCCTGATGGAACACCTTGTGGATTACTGAATCATATGACTCGTACTAGCC
                   tcttcacatttttcct  CT-rich tract
                                    ttttattgttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttctttcactttttacctgtcaaacactacatgtgctgatgctgtcccaaaattgtagtcttcacatttttcctcttttattgttatcttgtagATCTTGGGGTTTTCTTTGCCCTGTTCACACTCCTGATGGAACACCTTGTGGATTACTGAATCATATGACTCGTACTAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA