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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcacttattcctcatcttttcttccagagatgtggagtagtccacagtatccagtatatttcgttattgaaagcaaattctctccattgatatagacatctatgttagatatgacttactaggttaaggtcattactttcagGCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTGAAAAAAGGATATGGAATGGAATGTGATTG

Basic information

species Arabidopsis thaliana
transcript AT4G14350.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 5
gtaagtttcacttattcctcatcttttcttccagagat--gtggagtagtccacagtatccagtatatttcgttattgaaagcaaattctctccattgatatagacatctatgttagatatgacttactaggttaaggtcattactttcagGCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTGAAAAAAGGATATGGAATGGAATGTGATTG
           ||| |    | |   | | |||   ||   | ||    ||  ||| || ||     | |  ||  |     ||   ||| |   |  ||  |  ||   || || | |   |  |  |   |    || | |  |||||||| || ||||| || || || || ||||| ||||| |||||||||||  | ||||| || ||||||||||| ||||||||
----------gttagtagctagcaaatgtgccaacaatcattagaaacttcttcagaattcacc---tgttattccttgtgtcattatctatttctcaatgcattcaga-attttcgtttccatgttttgactggcagttaatgatttcagGCATACTCCACTGTCGGTACACCGGACTACATTGCTCCAGAAGTTCTTCTAAAAAAGGGTTATGGAATGGAGTGTGATTG

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 5
gtaagtttcacttattcctcatcttttcttccagagatgtggagtagtccacagtatccagtat--atttcgttattgaaagcaaattctctccattgatatagacatctatgttagatatgacttactaggttaaggtcattactttcagGCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTGAAAAAAGGATATGGAATGGAATGTGATTG
                                             | |    |   ||  ||    | || ||| | | |||    |   | |  ||   | | ||  | |  || ||      || ||   ||    ||| ||||  ||||| ||||| ||||| || || ||||||||||||||||| ||||||||  |||| ||||||||||| ||||||||||||||
---------------------------------------------atttggtaacctcttgttctgactttgttttggcaagttgctgacccctgttttgacaaactacgacatttgaagc--ttttctttcttt---tcaatactg-cagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 5
gtaagtttcacttattcctcatcttttcttccagagatgtggagtagtccacagtatccagtat-atttcgttattgaaagcaaattctctccattgatatagacatctatgttagatatgacttactaggttaaggtcattactttcagGCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTGAAAAAAGGATATGGAATGGAATGTGATTG
                                             | |    |   ||  || | | || ||| |   |||    |   | |  |    | | ||  |    || || ||   ||      | ||   |        ||||| ||||| ||||| || || ||||||||||||||||| ||||||||  |||| ||||||||||| ||||||||||||||
-------------------------------------------acatttggtaacctcttgtctgactttgttttgacaagttgctgacccctgtgttgacaaactacggcatttgaaattttttttcttttcaataccg-------cagGCCTATTCTACAGTCGGAACACCTGACTATATTGCCCCCGAAGTTCTTCTGAAGAAAGGATATGGCATGGAATGTGATTG

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 6
gtaagtttcacttattcctcatcttttcttccagagatgtggagtagtccacagtatccagtatatttcgttattgaaagcaaattctctccattgatatagacatctatgttagatatgacttactaggttaaggtcattactttcagGCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTGAAAAAAGGATATGGAATGGAATGTGATTG
                       ||||    |||   ||   |||  ||     | |||  |   | |||  ||   | |  || | | |  ||||||   | ||| |    ||    |  ||| ||   ||    | ||      ||||| ||||| |||||||| || ||||| |||||||| |||||||||||  |||| |||||||||||  |||||||||||||
-----------------------ttttgcctcagttttgacaagttttc-----tttcccct---tctcgccat---acgataactatatagattgat---ggcattt----taagcttttctttct---ttgcaataatg-----cagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 5
gtaagtttcacttattcctcatcttttcttccagagatgtggagtagtccacagtatccagtatatttcgttattgaaagcaaattctctccattgatatagacatctatgttagatatgacttactaggttaaggtcattactttcagGCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTGAAAAAAGGATATGGAATGGAATGTGATTG
                                     | ||    |||      |  | ||| |  ||      ||       |   |  | ||  | || ||   | || |||    |  ||| ||   ||    | ||      ||||| ||||| |||||||| || ||||| |||||||| |||||||||||  |||| |||||||||||  |||||||||||||
------------------------------------ttttgcctcagttt----tgacaagttttctttccccctgtggctgtacgatgactatatagattgatggc-attttaagcttttctttct---ttgcaataatg-----cagGCCTATTCTACAGTTGGAACACCTGATTATATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG

upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtttcacttattcctcatcttttcttccagagatgtggagtagtccacagtatccagtatatttcgttattgaaagcaaattctctccattgatatagacatctatgttagatatgacttactaggttaaggtcattactttcagGCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTGAAAAAAGGATATGGAATGGAATGTGATTG
                                             | |        ||   ||||     |  ||       |     | | |     |||    | ||| | |  ||  ||||   |  ||    |       | ||||| ||||| || ||||| || |||||||| ||||| |||||||| ||| | || ||||||||||| ||||| ||||||||
-------------------------------------------tcactttgtttcctctgttataagaaatgtttatgcaggaccctgcgctaactgcataagggtttatatcaacta-aacttttgatattggaat-----actgcagGCCTATTCTACTGTTGGTACCCCTGACTACATTGCTCCAGAAGTGCTGCTTAAGAAAGGATATGGGATGGAGTGTGATTG

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|116396686|gb|EG439278.1|EG439278
EST:     GCACCCAACAAGAGCAATTACTAAACTGGCAGAGAAATAGAAGGATGCTT                         GCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTG
genomic: GCACCCAACAAGAGCAATTACTAAACTGGCAGAGAAATAGAAGGATGCTTgtaagtttca ... ttactttcagGCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatatagacatctatgttagatatgacttactaggttaaggtcattactttcagGCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTGAAAAAAGGATATGGAATGGAATGTGATTG
                         gacttac  putative branch site (score: 2)
                                             ttactttc  putative PPT
                 ttagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcacttattcctcatcttttcttccagagatgtggagtagtccacagtatccagtatatttcgttattgaaagcaaattctctccattgatatagacatctatgttagatatgacttactaggttaaggtcattactttcagGCTTATTCCACAGTTGGCACTCCTGACTATATTGCCCCAGAAGTTCTGTTGAAAAAAGGATATGGAATGGAATGTGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT