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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctttggataaaacataacctttcattttgtgaaaatttcatctaacgtatggacattggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAATTCGATCTAGTGTGGTCGATGGAGAGTGGTGAGCATATGCCTGACAAGG

Basic information

species Arabidopsis thaliana
transcript AT1G64970.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64970.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G035213_T01 (Zea mays), 3'ss of exon 2
------------gtagctttggataaaacataacctttcattttgtgaaaatttcatctaacgtatggacattggacttc---------tagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAATTCGATCTAGTGTGGTCGATGGAGAGTGGTGAGCATATGCCTGACAAGG
            |  |||     |   || |  | |   | ||  |  ||    |   |||||| |          |  |          ||| | |  | |||||||| |||||  |||| || || ||    || ||  | |||||||| |||||||| ||||||||||| ||||| ||||| |||||| 
gtgcccactgctgctgctcctcctcttacctctcttgcaaattgttataacggccggttaacgtctcccttccaccccgcgtgacggagcagGTTACTCTGCAAGTTGCTGATGCTCTGGAGCAACCGTTTCCTGACGGGCAGTTCGATCTGGTGTGGTCCATGGAGAGTGGCGAGCACATGCCGGACAAGA

upper sequence: AT1G64970.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G01680.1 (Glycine max), 3'ss of exon 2
---------------gtagctttggata---aaacataacctttcattttgtgaaaatttca----tctaacgtatg-------gacattggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAATTCGATCTAGTGTGGTCGATGGAGAGTGGTGAGCATATGCCTGACAAGG
               |||  ||  | |    ||     |   |  |||||    |  |||      |||| | | ||       |    || | ||  ||| ||||||  | ||||| || ||  |  | || ||||||   ||||| ||||| ||||| |||||||| ||||||||||| ||||||||||||||||| |
cacatgtagctagtagtactttaaggtttttaatttctagtatctattttacacatgtttttaatttctagcatttgctttcatgtgtctgtaattgcagGTTTCCTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG

upper sequence: AT1G64970.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G01690.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------gtagctttggataaaacataaccttt-cattttgtgaaaatttcatctaacgtatggacattggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAATTCGATCTAGTGTGGTCGATGGAGAGTGGTGAGCATATGCCTGACAAGG
                                                                    | | || || ||| || |  |  |    ||      | |||   || |    |   |    || | ||  ||| |||||| || ||||| || ||  |  | || ||||||   || ||  | || ||||| |||||||| ||||||||||| ||||||||||||||||| |
gtcttcatttctcgacatgtttttagtatttatatttacgcattccaaggttctttataacttctatagaatctatgcatataatactatataaatatacaagtataataatatttgctttcatgtttctgtaattgcagGTTTCCTTTCAGGTTGCTGACGCTCTACAGCAACCATTCTCTGACGGCCAGTTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG

upper sequence: AT1G64970.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G35680.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------------gtagctttggataaaacataacctttcattttgtgaaaatttcatcta-acgtatggacat-tggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAATTCGATCTAGTGTGGTCGATGGAGAGTGGTGAGCATATGCCTGACAAGG
                                                                                                              |||  |   ||   ||| |   ||| | |||     | || | |  |   ||| | || | || | ||  ||| ||||||  | ||||| || ||  |  | || ||||||   || || || || ||||| || ||||| ||||||||||| ||||||||||||||||| |
gtcttcatttctcgaaatgcatgtttttcatttctagtaccgaggttattaataacatgctacagaatctctgcacatgtagctagtagtactttaaggtttttaatttctagtatct-attttacacatgtttttaatttccagtatttgctttcatgtgtacgtacgtctgtaattgcagGTTTCCTTTGAGGTTGCTGACGCCCTAAAGCAACCATTCCCTGACGGGAAGTTTGATCTGGTATGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAG

upper sequence: AT1G64970.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ25322 (Selaginella moellendorffii), 3'ss of exon 2
-----gtagctttggataaaacataacctttcattttgtgaaaatttcatctaacgtatggacattggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAATTCGATCTAGTGTGGTCGATGGAGAGTGGTGAGCATATGCCTGACAAGG
     || |  ||| || ||| |||          ||| |    |||| |||             |||| ||| |||  || || ||||| |||||||| ||| | ||||| ||   |||     |||| ||||| ||||||||||||||||| || ||||||||||| |||||| 
gtttcgttggcttgtatgaaatatagtgaactgacttgagtgt-tttcttct------------ctggatttc-agGTGTCGTTTCAAGTCGCGGATGCTTTGAACCAGCCGTTTCCAGACAACGAATTTGATCTCGTGTGGTCGATGGAGAGCGGGGAGCATATGCCAGACAAGC

upper sequence: AT1G64970.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ23345 (Selaginella moellendorffii), 3'ss of exon 2
-----gtagctttggataaaacataacctttcattttgtgaaaatttcatctaacgtatggacattggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAATTCGATCTAGTGTGGTCGATGGAGAGTGGTGAGCATATGCCTGACAAGG
     || |  ||| || |||  ||          ||| |    |||| |||             |||| ||| |||  || || ||||| |||||||| |||   ||||| ||   |||     |||| ||||| ||||||||||||||||| || ||||||||||| |||||| 
gttttgttggcttgtatgaaatgtagtgaactgacttgagtgt-tttcttct------------ctggatttc-agGTGTCGTTTCAAGTCGCGGATGCTTTGATCCAGCCGTTTCCAGACAACGAATTTGATCTCGTGTGGTCGATGGAGAGCGGGGAGCATATGCCAGACAAGC

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|86030505|gb|DR326258.1|DR326258
EST:     AGGCCAAGAGAGCCAATGATCTCGCGGCTGCTCAATCACTCTCTCATAAG                         GCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGA
genomic: AGGCCAAGAGAGCCAATGATCTCGCGGCTGCTCAATCACTCGCTCATAAGgtagctttgg ... ggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGA
EST: gi|86030506|gb|DR326259.1|DR326259
EST:     NNNCCAAGAGAGCCAATGATCTCGCGGCTGCTCAATCACTCTCTCATAAG                         GCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAA
genomic: AGGCCAAGAGAGCCAATGATCTCGCGGCTGCTCAATCACTCGCTCATAAGgtagctttgg ... ggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAA
EST: gi|86030490|gb|DR326243.1|DR326243
EST:     AGGCCAAGAGAGCCAATGATCTCGCGGCTGCTCAATCACTCTCTCATAAG                         GCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAA
genomic: AGGCCAAGAGAGCCAATGATCTCGCGGCTGCTCAATCACTCGCTCATAAGgtagctttgg ... ggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAA
EST: gi|86030471|gb|DR326224.1|DR326224
EST:     AGGCCAAGAGAGCCAATGATCTCGCGGCTGCTCAATCACTCTCTCATAAG                         GCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAA
genomic: AGGCCAAGAGAGCCAATGATCTCGCGGCTGCTCAATCACTCGCTCATAAGgtagctttgg ... ggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAA
EST: gi|86030498|gb|DR326251.1|DR326251
EST:     AGGCCAAGAGAGCCAATGATCTCGCGGCTGCTCAATCACTCTCTCATAAG                         GCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAA
genomic: AGGCCAAGAGAGCCAATGATCTCGCGGCTGCTCAATCACTCGCTCATAAGgtagctttgg ... ggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataacctttcattttgtgaaaatttcatctaacgtatggacattggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAATTCGATCTAGTGTGGTCGATGGAGAGTGGTGAGCATATGCCTGACAAGG
                           atctaac  putative branch site (score: 2)
                                                cttct  putative PPT
           attttgtgaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctttggataaaacataacctttcattttgtgaaaatttcatctaacgtatggacattggacttctagGCTTCCTTCCAAGTTGCGGATGCGTTGGATCAGCCATTCGAAGATGGAAAATTCGATCTAGTGTGGTCGATGGAGAGTGGTGAGCATATGCCTGACAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA