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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggatgagattagctattaatttgccttttattatttaagaaatttcattgtggcctcttcagtttcttatcatttctaaagcatggctactggcaattaatgtttgttcatttgcttattgtcaagattagtgctaagtagcgttgtcagctaatctcccttcgctggatacatgcagGTTGCTGCGTCAGAAGCAGGAGGAATTACACAAGGAATTGGTGCATATAAGGTGTCAGTGCCTGTTGATGGAAAGTTGCAGTCCTGCGTTTTCCTTGATA

Basic information

species Arabidopsis thaliana
transcript AT1G17220.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv19s0027g00130.t01 (Vitis vinifera), 3'ss of exon 2
gtatggatgagattagctattaatttgccttttattatttaagaaatttcattgtggcctcttcagtttcttatcatttctaaagcatggctactggcaattaatgtttgttcatttgcttattgtcaagattagtgctaagtagcgttgtcagctaatctcccttcgctggatacatgcagGTTGCTGCGTCAGAAGCAGGAGGAATTACACAAGGAATTGGTGCATATAAGGTGTCAGTGCCTGTTGATGGAAAGTTGCAGTCCTGCGTTTTCCTTGATA
                                                                           | |   |||  |    || |   ||  ||| ||     |     ||  |||      |  |     | |   |  |||  | |  ||     ||| |||   |||||||  |||| || ||||||||||| ||||||||||||||||||||||||||||| | ||||||  | ||||| |||   ||||| || |||||||||||||
-------------------------------------------------------------------------atactctaaaacta----tatttataacaaatattcag--agccattttatgttggccctgatat---gcacattattcaattgaagtctgactgctagatgtctgcagGTAACTGCATCGGAAGCAGGAGGGATTACACAAGGAATTGGTGCATATAAGGTTTTAGTGCCCATCGATGGCAAGCCACAGTCATGTGTTTTCCTTGATA

upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ26137 (Selaginella moellendorffii), 3'ss of exon 2
gtatggatgagattagctattaatttgccttttattatttaagaaatttcattgtggcctcttcagtttcttatcatttctaaagcatggctactggcaattaatgtttgttcatttgcttattgtcaagattagtgctaagtagcgttgtcagctaatctcccttcgctggatacatgcagGTTGCTGCGTCAGAAGCAGGAGGAATTACACAAGGAATTGGTGCATATAAGGTGTCAGTGCCTGTTGATGGAAAGTTGCAGTCCTGCGTTTTCCTTGATA
                                                                                                        | ||| ||  ||   |  ||       ||  || |   |   |||   || |  ||| | |||         || ||||| |||||   |||||| |||||||| ||||||| ||||||||||||| | ||| | ||| | || |||||  ||  |||  | || ||||||||||| |
-------------------------------------------------------------------------------------------------------gtatttcttttttctttcttttctttcctttttggtttctcatgttagaagttc-tctgcattcatg------attcagGTGGCTGCCGGAGAAGCTGGAGGAATCACACAAGCAATTGGTGCATATCAAGTGCCTGTGACAGTCGATGGGGAGGAGCAAACGTGTGTTTTCCTTGACA

upper sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ10805 (Selaginella moellendorffii), 3'ss of exon 2
gtatggatgagattagctattaatttgccttttattatttaagaaatttcattgtggcctcttcagtttcttatcatttctaaagcatggctactggcaattaatgtttgttcatttgcttattgtcaagattagtgctaagtagcgttgtcagctaatctcccttcgctggatacatgcagGTTGCTGCGTCAGAAGCAGGAGGAATTACACAAGGAATTGGTGCATATAAGGTGTCAGTGCCTGTTGATGGAAAGTTGCAGTCCTGCGTTTTCCTTGATA
                                                                                                         || | |   |||  || || ||  | ||  |  |   |     |||  |  ||  || || |  |  ||  || ||||| |||||   |||||| |||||||| ||||||| ||||||||||||| | ||| | ||| | || |||||  ||  |||  | || ||||||||||| |
---------------------------------------------------------------------------------------------------------gtatttctttttctttcttttc--gtttcttttttgtttctcatgtagg--aagttctctgcattc-atg-attcagGTGGCTGCCGGAGAAGCTGGAGGAATCACACAAGCAATTGGTGCATATCAAGTGCCTGTGACAGTCGATGGGGAGGAGCAAACGTGTGTTTTCCTTGACA

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|47831587|gb|CK121271.1|CK121271
EST:     ACCACTCTTCTCGACTATATCAGAAAAAGCAAG                         GTTGCTGCGTCAGAAGCAGGAGGAATTACACAAGGAATTGGTGCATATAAG
genomic: ACCACTCTTCTCGACTATATCAGAAAAAGCAAGgtatggatga ... atacatgcagGTTGCTGCGTCAGAAGCAGGAGGAATTACACAAGGAATTGGTGCATATAAG
EST: gi|125283743|gb|EL297828.1|EL297828
EST:     ACCACTCTTCTCGACTATATCAGAAAAAAGCAAG                         GTTGCTGCGTCAGAAG
genomic: ACCACTCTTCTCGACTATATCAGAAAAA-GCAAGgtatggatga ... atacatgcagGTTGCTGCGTCAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagattagtgctaagtagcgttgtcagctaatctcccttcgctggatacatgcagGTTGCTGCGTCAGAAGCAGGAGGAATTACACAAGGAATTGGTGCATATAAGGTGTCAGTGCCTGTTGATGGAAAGTTGCAGTCCTGCGTTTTCCTTGATA
                         agctaat  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggatgagattagctattaatttgccttttattatttaagaaatttcattgtggcctcttcagtttcttatcatttctaaagcatggctactggcaattaatgtttgttcatttgcttattgtcaagattagtgctaagtagcgttgtcagctaatctcccttcgctggatacatgcagGTTGCTGCGTCAGAAGCAGGAGGAATTACACAAGGAATTGGTGCATATAAGGTGTCAGTGCCTGTTGATGGAAAGTTGCAGTCCTGCGTTTTCCTTGATA

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