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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtggtcatagtacctgtaaaacttattcaagcttttactactctcttctggagtaaaaaacttttgttttggacgcagGATCAGAGAGTCCCGGAACAGAGGCAAATGGGAACGCCTACGATTTCACAACAAAGTTGCTGCATATGGCTTGGCACCCAACAGAGAACTCAATTGCTTG

Basic information

species Arabidopsis thaliana
transcript AT1G17720.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G20830.1 (Glycine max), 3'ss of exon 13
------------gttagtggtcata---gtacctgtaaaactta-ttcaagcttttactactctcttctgga----gtaaaaaacttttgttttggacgcagGATCAGAGAGTCCCGGAACAGAGGCAAATGGGAACGCCTACGATTTCACAACAAAGTTGCTGCATATGGCTTGGCACCCAACAGAGAACTCAATTGCTTG
             |||       ||   ||   |  |  |  ||  |    ||| |  || |    ||        | || | | |  | || | ||  ||||| |||||||  ||||    || |||||||||||  | |  |||||||||||||||||||||||  | || ||||||||||| ||||| |||||||||||
gtaagttctctatttaacaactttatttgtgttttcatgatatagcttgttcttcttgtagtaatatcaaagacttgcaatacattggtattcttga-acagGAGCAGAGAGCGCCGGTGTTGACGCAAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCACCCAACTGAGAATTCAATTGCTTG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 13
--------gttagtggtcata---gtacctgtaaaactta-ttcaagcttttactactctcttctgga----gtaaaaaacttttgttttggacgcagGATCAGAGAGTCCCGGAACAGAGGCAAATGGGAACGCCTACGATTTCACAACAAAGTTGCTGCATATGGCTTGGCACCCAACAGAGAACTCAATTGCTTG------
         |||       ||   ||   |  |  |  ||  |    ||| |  || |    ||        | || | | |  | || | ||  ||||| |||||||  ||||    || |||||||||||  | |  |||||||||||||||||||||||  | || ||||||||||| ||||| |||||||||||      
gttctctatttaacaactttatttgtgttttcatgatatagcttgttcttcttgtagtaatatcaaagacttgcaatacattggtattcttga-acaggagcagAGAGCGCCGGTGTTGACGCAAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCACCCAACTGAGAATTCAATTGCTTGTGCTGC

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 13
gttagtggtcatagtacc-----tgtaaaacttattcaagcttttactactctcttctggagtaa---aaaactt---ttgttttgg-------acgcagGATCAGAGAGTCCCGGAACAGAGGCAAATGGGAACGCCTACGATTTCACAACAAAGTTGCTGCATATGGCTTGGCACCCAACAGAGAACTCAATTGCTTG
|| |||  |||   || |     ||   || || ||      | ||   ||   |  || ||||    || ||||    | | ||||          ||||| |||| ||| || |    || |||||||||||  | |  |||||||||||||||||||||||  | || ||||||||||| ||||| |||||||||||
gtaagttctcaatttatcaactttgcccaagtttttatgatatatatagcttgttcttgtagtatatcaagacttgcaatatattggtaatcttgaacagGAGCAGAAAGTGCCAGTGTCGACGCAAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCACCCAACTGAGAATTCAATTGCTTG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 13
--------------------gttagtggtcatagtacctgtaaaacttattcaagcttttactac--tctcttctggagtaaaaaacttt--tgttttggacgcagGATCAGAGAGTCCCGGAACAGAGGCAAATGGGAACGCCTACGATTTCACAACAAAGTTGCTGCATATGGCTTGGCACCCAACAGAGAACTCAATTGCTTG
                         || |    |   |  ||||  || ||     | ||||||   | |  ||  ||||   ||  |||  | || | ||  ||||| |||| |  || |||   || || ||||||||  | |  |||||||||||||||||||||||  | || ||||| ||||  ||||| |||||||||||
gtcagttttctttttcattttcccttgtttgatgattccataaatattttttggtttgttactataatattgtcaagagtctcaatatttgatattcttga-acagGAGCAGAAACCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG

upper sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 13
----------------------------gttagt-ggtcatagtacctgtaaaacttattcaagcttttactac--tctcttctggagtaaaaaacttt--tgttttggacgcagGATCAGAGAGTCCCGGAACAGAGGCAAATGGGAACGCCTACGATTTCACAACAAAGTTGCTGCATATGGCTTGGCACCCAACAGAGAACTCAATTGCTTG
                             | | | |  || ||   |  ||||  ||  |     | ||||||   | |  ||   |||   ||  ||   | || | ||  ||||| ||||    || |||   || || ||||||||  | |  |||||||||||||||||||||||  | || ||||| ||||  ||||| |||||||||||
gtcagttttctttttcattttcccttgtatgatttgagcaaagattccataaatatttattggtttgttactataatgttgtcacaagtctcaatattcgatattcttga-acagGAGCAGAAGCCCCTGGAGTGGATGCTAATGGGAATTCTTTTGATTTCACAACAAAGTTGCTGCACTTAGCATGGCATCCAAGTGAGAATTCAATTGCTTG

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|125257166|gb|EL271251.1|EL271251
EST:     TATGACACGCGTGGTTAGACGAG                         GATCAGAGAGTCCCGGAACAGAGGCAAATGGGAACGCCTACGATTTCACAA
genomic: TATGACACGCGTGGTTAGACGAGgttagtggtc ... ttggacgcagGATCAGAGAGTCCCGGAACAGAGGCAAATGGGAACGCCTACGATTTCACAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcaagcttttactactctcttctggagtaaaaaacttttgttttggacgcagGATCAGAGAGTCCCGGAACAGAGGCAAATGGGAACGCCTACGATTTCACAACAAAGTTGCTGCATATGGCTTGGCACCCAACAGAGAACTCAATTGCTTG
                                     cttttgtttt  CT-rich tract
                              taaaaaacttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtggtcatagtacctgtaaaacttattcaagcttttactactctcttctggagtaaaaaacttttgttttggacgcagGATCAGAGAGTCCCGGAACAGAGGCAAATGGGAACGCCTACGATTTCACAACAAAGTTGCTGCATATGGCTTGGCACCCAACAGAGAACTCAATTGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC