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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCTTGGTTCACAGTGGAGGAGTGCATGGAGGGCATTATTATGCTTTTATTAGGCCAACACTTTCAGATCAGTGgtatgtacccttcaactcttttatgctaaaatacgttttgtattttgtaatcttgacgtatttttttatattgcaaactagttttctcgtcatctaggct...

Basic information

species Arabidopsis thaliana
transcript AT3G11910.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11910.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 11
TGTCTTGGTTCACAGTGGAGGAGTGCATGGAGGGCATTATTATGCTTTTATTAGGCCAACACTTTCAGATCAGTGgtatgtacccttcaactcttttatgctaaaatacgttttgtattttgtaatcttgacgtatttttttatattgcaa-actagttttctcgtcatctaggct------
|||  | ||||| ||||||||||| ||||| || || || |||||||| ||| |||| ||||| || |||||||||| |||    ||| | |||  |  | |  | | | || ||       | |  ||||  || ||||   |  ||||  | || |||  | ||   |  |  |      
TGTTCTTGTTCATAGTGGAGGAGTACATGGTGGTCACTACTATGCTTTCATTCGGCCGACACTCTCGGATCAGTGgtgtgt----ttcta-tctcatgagtttcagttcattctggtacagttcacattga--tagttttccgttctgcaccattattttgattgtggcccggcattttaag

upper sequence: AT3G11910.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 11
TGTCTTGGTTCACAGTGGAGGAGTGCATGGAGGGCATTATTATGCTTTTATTAGGCCAACACTTTCAGATCAGTGgtatgtacccttcaactc----ttttatgctaaaatacgttttgtattttgtaatcttgacgtatttttttatattgcaaactagttttctcgtcatctaggct--
||| |||||||| || || || |||||||| || ||||||||||||||||| ||||| || ||||| ||||||||||||| | | |  |        |||| |||||| | || || |||   ||   || ||    |   |    |   |  |||      ||| |     || || |  
TGTTTTGGTTCATAGCGGTGGTGTGCATGGTGGACATTATTATGCTTTTATCAGGCCGACCCTTTCTGATCAGTGgtatgcatcatatactataagattttttgctaata-actttgtgtgcatttgcatattt---tgcatccggaagctagaaatc--ccttcacagtcgctgggtttg

upper sequence: AT3G11910.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 5'ss of exon 11
TGTCTTGGTTCACAGTGGAGGAGTGCATGGAGGGCATTATTATGCTTTTATTAGGCCAACACTTTCAGATCAGTGgtatgtacccttcaactcttttatgctaaaatacgttttgtattttgtaatcttgacgtatttttttatattgcaaactagttttctcgtcatctaggct------
|||  ||||||||||||| ||||| ||||| || ||||| || |||||||| || || ||||| || || ||||||||| |   || ||     |  |  |  || |     |||| |||  |  |     |||  ||   | |       ||| || || |     |  | |        
TGTACTGGTTCACAGTGGTGGAGTACATGGTGGTCATTACTACGCTTTTATCAGACCCACACTCTCTGACCAGTGgtattttttctgca-----tcaactcgtaattgtcggttgtctttgcttctacgagcgtggttacatgtgc-atggactcgtattttaaaagtagaagtcggtttc

upper sequence: AT3G11910.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ13603 (Selaginella moellendorffii), 5'ss of exon 10
------------------------------------------------------------------------------------------------------------------------------------------------------------TGTCTTGGTTCACAGTGGAGGAGTGCATGGAGGGCATTATTATGCTTTTATTAGGCCAACACTTTCAGATCAGTGgtatgtacccttcaactcttttatgctaaaatacgttttgtattttgtaatcttgacgtatttttttatattgcaaactagttttctcgtcatctaggct
                                                                                                                                                            |||| |||||||||| ||||| || || ||||| || ||||||||||||||  |||| |||||||| ||||| ||||  ||  | |||     | || ||   | | |   ||| ||       || |  |                                            
GGTACGAGTTTCCTTTGGAGTTGGACTTGGACAGAGAAGACGGGAAGTATTTGTCCCCTGACGCAGATAGAAGTGTGCGGAATCTATATACTTTACACAGgtagcgtatatgttttgggccttcgcattgcagtacggtaataagtgcaagtgcagtgtcctggttcacagcggaggggttcacggaggacactattatgcttttatccggcctacactttccgatcaatggtgggtgtcgttcgctgttgttttgtggagacaaactttataacggactatttgcag-------------------------------------------

upper sequence: AT3G11910.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ19227 (Selaginella moellendorffii), 5'ss of exon 11
TGTCTTGGTTCACAGTGGAGGAGTGCATGGAGGGCATTATTATGCTTTTATTAGGCCAACACTTTCAGATCAGTGgtatgtacccttcaactcttttatgctaaaatacgttttgtattttgtaatcttgacgtatttttttatattgcaaactagttttctcgtcatctaggct
|||| |||||||||| ||||| || || ||||| || ||||||||||||||  |||| |||||||| ||||| ||||  ||  | |||     | || ||   | | |   ||| ||       || |  |                                            
TGTCCTGGTTCACAGCGGAGGGGTTCACGGAGGACACTATTATGCTTTTATCCGGCCTACACTTTCCGATCAATGgtgggtgtcgttcgctgttgttttgtggagacaaactttataacggactatttgcag-------------------------------------------

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|125192462|gb|EL207416.1|EL207416
EST:     CATGGAGGGCATTATTATGCTTTTATTAGGCCAACACTTTCAGATCAGTG                         GTATAAATTTGACGATGAACGGGTCACGAAA
genomic: CATGGAGGGCATTATTATGCTTTTATTAGGCCAACACTTTCAGATCAGTGgtatgtaccc ... attctttcagGTATAAATTTGACGATGAACGGGTCACGAAA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCTTGGTTCACAGTGGAGGAGTGCATGGAGGGCATTATTATGCTTTTATTAGGCCAACACTTTCAGATCAGTGgtatgtacccttcaactcttttatgctaaaatacgttttgtattttgtaatcttgacgtatttttttatattgcaaactagttttctcgtcatctaggct

- - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctttta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcgtca