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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaattttatgtttctataaccctttcaaggtctagtacagtgtgttcctgaatgttaatcatagcttgttgttggtttttcccttcttgagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGATAGTTAAGCGCCGGGGACGAATCTATGTGATTTGCTCTGGGAACCCTAA

Basic information

species Glycine max
transcript GLYMA17G12290.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12290.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G20180.2 (Arabidopsis thaliana), 3'ss of exon 2
-----------tggaattttatgtttc-----tataaccctt-----------tcaaggtctagtac-----agtgtgttcctgaatgttaatc--atagctt----gttgttggtttttcccttcttgagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGATAGTTAAGCGCCGGGGACGAATCTATGTGATTTGCTCTGGGAACCCTAA
            | |||  |||||||      || || ||||           | || ||  | |||     || ||  || |  || || |||  ||   ||    |||  || |   |      |||   | | |||||| ||||||||| | ||||||||||||||||||||||| |||||| | | ||| || || || |||||  | ||||| || ||||||   ||      
gtagattaagtagaaatgatatgtttagaggatacaatccttagttttgaatcttaaagttgaatactttgaagagttctctttcattttcatctaatgagttttgtgttaatgatcggttgtgaattgcagAGTGAGAAGCAATGAAGGTGAGATCATCTGTGAAGAAGATGTGTGAGTTTTGTAAAACAGTGAAACGTCGTGGACGTGTGTATGTTATATGCTCTTCCAA------

upper sequence: GLYMA17G12290.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G20180.1 (Arabidopsis thaliana), 3'ss of exon 1
tggaattttatgtttctataaccctttcaaggtctagtacagtgtgttcctgaatgttaatc--atagctt----gttgttggtttttcccttcttgagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGATAGTTAAGCGCCGGGGACGAATCTATGTGATTTGCTCTGGGAACCCTAA
|  |||  |  ||||  |              |    |  || ||  || |  || || |||  ||   ||    |||  || |   |      |||   | | |||||| ||||||||| | ||||||||||||||||||||||| |||||| | | ||| || || || |||||  | ||||| || ||||||   ||      
tacaatccttagttttgaatcttaaagttgaatactttgaagagttctctttcattttcatctaatgagttttgtgttaatgatcggttgtgaattgcagAGTGAGAAGCAATGAAGGTGAGATCATCTGTGAAGAAGATGTGTGAGTTTTGTAAAACAGTGAAACGTCGTGGACGTGTGTATGTTATATGCTCTTCCAA------

upper sequence: GLYMA17G12290.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g05390.t01 (Vitis vinifera), 3'ss of exon 1
tggaattttatgtttctataaccctttcaaggtctagtacagtgtgttcctgaatgt-taatcatagcttg------ttgttggtttttcccttcttgagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGATAGTTAAGCGCCGGGGACGAATCTATGTGATTTGCTCTGGGAACCCTAA
     || |   |||   ||    ||   |  | || | |  |   ||  |  |||| | || || |  |       ||| ||  || |   |||   |    |||| ||||||||||||||| ||||| |||||||| |||||||| | ||||   | ||| || || || || ||| | |||||  | ||| | |  || || ||
-----ttcttcattttactagtgtttgtgaaatttatttccttacattggttcatgtgtgattattgactagaaggtttgatgagttcttaattcc--aatcttcagTAGCCATGAAGGTGCGATCATCAGTGAAGAAAATGTGTGAGTATTGTAGAACAGTCAAACGTCGTGGGCGAGTATATGTACTATGCACAGCCAATCCCAA

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|17020758|gb|BM091792.1|BM091792
EST:     TTCTTTCAGTTGCCATATACCCTCTCTCTTTACCTCTCAGACACTACAAG                         AAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
genomic: TTCTTTCAGTTGCCATATACCCTCTCTCTTTACCTCTCAGACACTACAAGgttcgtcttt ... gagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
EST: gi|298191145|gb|HO038624.1|HO038624
EST:     TTCTTTCAGTTGCCATATACCCTCTCTCTTTACCTCTCAGACACTACAAG                         AAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
genomic: TTCTTTCAGTTGCCATATACCCTCTCTCTTTACCTCTCAGACACTACAAGgttcgtcttt ... gagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
EST: gi|19934906|gb|BQ079936.1|BQ079936
EST:     CTTTACCTCTCAGACACTACAAG                         AAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
genomic: CTTTACCTCTCAGACACTACAAGgttcgtcttt ... gagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
EST: gi|14125779|gb|BG790217.1|BG790217
EST:     TACCCTCTCTCTTTACCTCTCAGACACTACAAG                         AAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
genomic: TACCCTCTCTCTTTACCTCTCAGACACTACAAGgttcgtcttt ... gagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
EST: gi|13181351|gb|BG352752.1|BG352752
EST:     CATATACCCTCTCTCTTTACCTCTCAGACACTACAAG                         AAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
genomic: CATATACCCTCTCTCTTTACCTCTCAGACACTACAAGgttcgtcttt ... gagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
EST: gi|9820852|gb|BE556362.1|BE556362
EST:     TACCCTCTCTCTTTACCTCTCAGACACTAC---                         AAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
genomic: TACCCTCTCTCTTTACCTCTCAGACACTACAAGgttcgtcttt ... gagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
EST: gi|7640110|gb|AW734418.1|AW734418
EST:     TTCTTTCAGTTGCCATATACCCTCTCTCTTTACCTCTCAGACACTACAAG                         AAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA
genomic: TTCTTTCAGTTGCCATATACCCTCTCTCTTTACCTCTCAGACACTACAAGgttcgtcttt ... gagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcctgaatgttaatcatagcttgttgttggtttttcccttcttgagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGATAGTTAAGCGCCGGGGACGAATCTATGTGATTTGCTCTGGGAACCCTAA
         tgttaat  putative branch site (score: 3)
                                tttttcccttcttg  putative PPT
       aatgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggaattttatgtttctataaccctttcaaggtctagtacagtgtgttcctgaatgttaatcatagcttgttgttggtttttcccttcttgagaactcagAAGCCATGAAGGTGCGGTCATCTGTGAAGAAGATGTGTGAATTTTGTCAGATAGTTAAGCGCCGGGGACGAATCTATGTGATTTGCTCTGGGAACCCTAA

- - - - - - - - - - -ccctttc
- - - - - - - - - - - - - - - - - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - tgaatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgtt