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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgttttccccatttttgttttcttataacaacaacatatagtcgacttagcgcgttctgttttcacgatttcagATCGAAATGTTATCGAAGATCAACCACAAGAATTTTGCAAACCTTCTTGGTTATTGTGAAGAAAAGGAACCTTTCACCAGGATCTTGATCTTTGAGTATG

Basic information

species Arabidopsis thaliana
transcript AT2G40270.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G40270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G02850.1 (Glycine max), 3'ss of exon 7
----------gtattgttttccccatttttgttttcttataacaacaa--catatagtcgacttagcgcgttctgttttcacgatttcagATCGAAATGTTATCGAAGATCAACCACAAGAATTTTGCAAACCTTCTTGGTTATTGTGAAGAAAAGGAACCTTTCACCAGGATCTTGATCTTTGAGTATG
           ||     |   | |||| | ||||    |  |||| |  |   || |  |  || |   ||  |   | | | |||||||| || |  ||||| ||  | |||||||||||||||| ||| ||||||||  ||||||||||| | || ||||||||||| ||  || | ||||||||||
gtactgccaactaaaacataaacaatttcttttttagattttcaactaggctgctattgtaactaacattttaagcaattatggtttcagATAGATACATTATCAAAAGTGAACCACAAGAATTTTGTAAATCTTCTTGGACATTGTGAAGAAGATGAGCCTTTCACCAGAATGGTGGTTTTTGAGTATG

upper sequence: AT2G40270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G35570.1 (Glycine max), 3'ss of exon 6
---------------gtattgttttccccatttttgttttcttataacaacaacatatagtcgacttagcgcgttctgttttcacgatttcagATCGAAATGTTATCGAAGATCAACCACAAGAATTTTGCAAACCTTCTTGGTTATTGTGAAGAAAAGGAACCTTTCACCAGGATCTTGATCTTTGAGTATG
                 ||     |     |||||||    ||  ||  |       || |  |  ||     ||  |   | | |||||||||| || |  ||||| ||  | |||||||||||||||| ||| ||||||||  ||||||||||| | || ||||||||||| ||  || | ||||||||||
gtactaccacctaaaacataaacatttatttttttgtagatttccaattaggctgc-tattgtaactaatattttaagcaattatgatttcagATAGATACATTATCAAAAGTGAACCACAAGAATTTTGTAAATCTTCTTGGACATTGTGAAGAAGATGAGCCTTTCACCAGAATGGTGGTTTTTGAGTATG

upper sequence: AT2G40270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G43150.1 (Glycine max), 3'ss of exon 8
--------------------gtattgttttccccatttttgttttcttataacaac----aacatatagtcg--acttagcgcgttctgttttcacgatttcagATCGAAATGTTATCGAAGATCAACCACAAGAATTTTGCAAACCTTCTTGGTTATTGTGAAGAAAAGGAACCTTTCACCAGGATCTTGATCTTTGAGTATG
                    | |         | | |||   | |   ||  |||      | || || |    ||| |   | |     |  || |  ||||||| || |  || |||||  | ||||||||||||||||  || ||| |||| || ||||||||| |||| |||||||||||  | ||| | ||||| ||||
gtacaccaattattataacagaaaaaacccagcaaatttaactgtagaattgcaattcaggaaatttaattataactaacttcttaaccataccatggcttcagATAGATACATTGTCGAAAGTGAACCACAAGAATTTTGTCAATCTTATTGGATACTGTGAAGAAGAGGATCCTTTCACCAGAGTGTTGGTTTTTGAATATG

upper sequence: AT2G40270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G06230.1 (Glycine max), 3'ss of exon 7
-----------------------------gtattgttttccccatttttgttttcttataacaacaacatatagtcgac--ttagcgcgttct--gttttcacgatttcagATCGAAATGTTATCGAAGATCAACCACAAGAATTTTGCAAACCTTCTTGGTTATTGTGAAGAAAAGGAACCTTTCACCAGGATCTTGATCTTTGAGTATG
                               |         | | |||   | |   ||  |||      | | | ||   |||     ||||      ||| | |||||||| || |  || |||||  | ||||||||||||||||  || ||| |||| || ||||||||| |||| ||||||||||| || ||| | ||||| ||||
gtacgtcaattatcataacagaaaagaaaaaaaaaacccagcaaatttaactgtagaattgcaatttaggaaatttgattattactaacttcttaaccatcatggtttcagATAGATAAATTGTCGAAAGTGAACCACAAGAATTTTGTGAATCTTATTGGATACTGTGAAGAAGAGGAGCCTTTCACCAGAATGTTGGTTTTTGAATATG

upper sequence: AT2G40270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0067g01550.t01 (Vitis vinifera), 3'ss of exon 7
gtatt-----gttttccccatttttgttttcttataacaacaacatatagtcgacttagcgcgttctgttttcacgatttcagATCGAAATGTTATCGAAGATCAACCACAAGAATTTTGCAAACCTTCTTGGTTATTGTGAAGAAAAGGAACCTTTCACCAGGATCTTGATCTTTGAGTATG
||| |     | || |  |   |    ||| |  |    |       | || | | |  |   |||| |  |   | ||||||||||||| |||||| ||  | ||||||||||||||||  |||||||| || |||||||||||| |||||||||||||||| ||  || | ||||| ||||
gtacttgagagattacatccactaaactttgtggttttgattcatcttggtagtccttacattttctttggttgtggtttcagATCGAAAGGTTATCAAAAGTGAACCACAAGAATTTTGTCAACCTTCTCGGATATTGTGAAGAAGAGGAACCTTTCACCAGAATGATGGTTTTTGAATATG

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|124760874|gb|EH851004.1|EH851004
EST:     TACTGCCAAAGACTGGAAGGACAGTACAGAAATTCACTTCAGGAAAGAAG                         ATCGAAATGTTATCGAAGATCAACC
genomic: TACTGCCAAAGACTGGAAGGACAGTACAGAAATTCACTTCAGGAA-GAAGgtattgtttt ... acgatttcagATCGAAATGTTATCGAAGATCAACC
EST: gi|125224532|gb|EL238617.1|EL238617
EST:     CTACTGCCAAAGACTGGAAGGACAGTACAGAAATTCACTTCAGGAAGAAG                         ATCGAAATGTTATCGAAGATCAACC
genomic: CTACTGCCAAAGACTGGAAGGACAGTACAGAAATTCACTTCAGGAAGAAGgtattgtttt ... acgatttcagATCGAAATGTTATCGAAGATCAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttataacaacaacatatagtcgacttagcgcgttctgttttcacgatttcagATCGAAATGTTATCGAAGATCAACCACAAGAATTTTGCAAACCTTCTTGGTTATTGTGAAGAAAAGGAACCTTTCACCAGGATCTTGATCTTTGAGTATG
   ttataac  putative branch site (score: 2)
                                        ttttcac  putative PPT
             aacatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgttttccccatttttgttttcttataacaacaacatatagtcgacttagcgcgttctgttttcacgatttcagATCGAAATGTTATCGAAGATCAACCACAAGAATTTTGCAAACCTTCTTGGTTATTGTGAAGAAAAGGAACCTTTCACCAGGATCTTGATCTTTGAGTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA