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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttctcccatcacagatgcctcctaatcctattaatcatcaaaagaacttgcattttcaaatatggttagtttactaaaccgtgtcgttgaatttttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG

Basic information

species Glycine max
transcript GLYMA02G47140.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G47140.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 2
acttctcccat-cacagatgcctcctaatcctattaatcatcaaaagaacttgcattttcaaatatggttagtttactaaaccgtgtcgttgaatttttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
         ||  | | |        |||   ||| |  |   | | |  ||   |||  ||     ||||  ||| | | | ||   ||         || || | || ||||||||||| || || ||||||| || ||| ||||| || || ||||||||||||||| |||| ||||| ||||| ||||| || ||
-------gtatgtatacacaatatacaatataattcaaaaattacatagtttttgtttgtaa---cagttacattatttatctgtcatgt---------agTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG

upper sequence: GLYMA02G47140.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G55930.1 (Arabidopsis thaliana), 3'ss of exon 2
acttctcccatcacagatgcctcctaatcctattaatcatcaaaagaacttgcattttcaaatatggttagtttactaaaccgtgtcgttgaattttt----agATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
          | | ||     |    |    |   ||   | ||  |||    ||||| ||  ||   |  | |   | ||  |  |  | | || ||    || || | || |||||||||||||| || |||||||  |||||||||||||| ||||| ||||||||||| |||||  | || ||||| || || || ||
----tgtgggtaatagtcatttaaatactagaactatggcctaagaaacaaatatttttaacgatttgtgatctttaagactttaacaatcatttcttttgcagTTGTTGGGATATGGATGGGCTGGAATCTTCAGGAAGTTCCTTGTGGATTCACCGTATATGTGGTGGCCGTCAAATTTGGTTCAAGTCTCACTCTTTAG

upper sequence: GLYMA02G47140.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0015g00860.t01 (Vitis vinifera), 3'ss of exon 2
acttctcccatcacagatgcctc-ctaatcctattaatcatcaaaagaacttgcattttcaaata----tggttagtttactaaaccgtgtcgttgaatt---tttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
          |   | |||  |  || || ||| |||||  | ||  || |||   ||| |  |     || | |  ||  ||     | |  ||  |||   || || ||||||| ||||||||||||||  | ||||| | || ||| ||||| ||||| || ||||||||||| ||||| || |||||||| ||||| |||||
--------tgtagtatatggtttactcatactactaatccaccaattaatttgatattttagtttctcttgttcaccttgatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG

upper sequence: GLYMA02G47140.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0015g00870.t01 (Vitis vinifera), 3'ss of exon 1
-------acttctcccatcacagatgcctcctaatcctattaatcatcaaaagaacttgcattttcaaatatggttagtttactaaaccgtgtcgttgaatttttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
       |||| |    |   | |||  | | |  || ||||||     |    | || |  ||    |  |   ||||||         |    |||||||   || ||||||| ||||||||||||||  | ||||| | || ||| ||||| ||||| || ||||||||||| ||||| || |||||||| ||||| |||||
atatattacttattttgtagtatatggtttcca--ccaattaatttgatattttaatttctcttgttgaccttcatagtttctc---ttcttctattgaatt--cagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG

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|208296021|gb|GE096121.1|GE096121
EST:     ACAGGAATATCCATCCACTTGCCGCTTTTCTCTTGGCACTTTCCACCCAG                         ATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCC
genomic: ACAGGAATATCCATCCACTTGCCGCTTTTCTCTTGGCACTTTCCACCCAGgtcaacatta ... gaatttttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCC
EST: gi|208214187|gb|GE014576.1|GE014576
EST:     ACAGGAATATCCATCCACTTGCCGCTTTTCTCTTGGCACTTTCCACCCAG                         ATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCC
genomic: ACAGGAATATCCATCCACTTGCCGCTTTTCTCTTGGCACTTTCCACCCAGgtcaacatta ... gaatttttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacttgcattttcaaatatggttagtttactaaaccgtgtcgttgaatttttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
                            tactaaa  putative branch site (score: 1)
                                                ttttt  putative PPT
        attttcaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttctcccatcacagatgcctcctaatcctattaatcatcaaaagaacttgcattttcaaatatggttagtttactaaaccgtgtcgttgaatttttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- ttctccc
- - - - - - - - -tgcctcc
- - - - - - - - - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaacc