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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttcaagtagtaaagtaattcttaatatttctgtgaatgctgagtaaatataagcaaagtttcttatgcgttttttccccttccactatgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG

Basic information

species Glycine max
transcript GLYMA08G20100.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 10
tctttcaagtag---taaagtaattcttaatatttctgtgaatgctgagtaaatataagcaaagtttcttatgcgttttttccccttccactatgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
   || ||||||   |||  |  |  ||  || |  | | || |  ||    | ||       | |  || ||    || ||   ||    | ||    |||||| |||||||| ||||| |||||| ||||||||||| |||||||   ||| || || || ||||||||||| ||||| ||||| ||  || | ||||| |
-tctttaagtaggactaactttgtctttgctaatcatat-aacgacgaaagtaaattgtagtggctatttttgaaagttgtctgtttttgtt-tgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 10
------tct-ttcaagtagtaaagtaattcttaatatttctgtgaatgctgagtaaatataagcaaagtttcttatgcgttttttccccttccactatgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
      ||| |||   || |  ||      || | |||| ||   |  ||| ||   | |     ||  || ||||||   |||     ||    | ||   ||||||| || ||||| |||||||| ||| | || |||||  |||||||||  |||||||| || ||||| ||||||||||||||||| || ||||| |||||||
taattctctgttcttttattggagatgccatttaaatttatgctga--ctgtgtt--tgtggcttaatcttattatgctgctttgtgattt---ttgtgctcaacagGTATATTATGTATATGGCTTTATGTTGCTTGTTTTCATGATTCTTATGATTGTTACAGTCTGTGTAACAATTGTGGGGACATATTTCTTGTTGAATGCTG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 10
-----tctttcaagtagtaaagtaattcttaatatttctgtgaatgctgagtaaat-ataagcaaagtttcttatgcgttttttccccttccactatgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
     ||| || | |  |  || |||||  | ||||  | |||  |  |   ||||  |  |||  |  |  ||  | |||||| |  ||    | ||     |||||||| |||||||||||||| |||||||||||||| |||||||| |  ||||| ||||||||||||||||| ||||| |||||||| ||| |||||||||
ctctctctctcta-tttttgagaaattcggactattgtt-tgacaggagttcaaattgtttgcagtggatgataaacattttttgctgtt----tgtgctgggcagGTGTATTATGTCTATGGCTTTATGCTACTGGTTTTCCTGATTCTCATAATTGTCACTGTTTGTGTGACAATAGTGGGAACATACTTCTTGCTAAATGCTG

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|10847708|gb|BF070348.1|BF070348
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
EST: gi|19935331|gb|BQ080361.1|BQ080361
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
EST: gi|9565317|gb|BE474826.1|BE474826
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
EST: gi|58015230|gb|CX701972.1|CX701972
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
EST: gi|16105838|gb|BI893578.1|BI893578
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
EST: gi|192331779|gb|FK024883.1|FK024883
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATACTACTGGTTTTTCTGATTCTTATCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgagttaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaatataagcaaagtttcttatgcgttttttccccttccactatgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
                         cgttttttccccttcc  CT-rich tract
                tttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttcaagtagtaaagtaattcttaatatttctgtgaatgctgagtaaatataagcaaagtttcttatgcgttttttccccttccactatgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - gaatgct
- - - - - - - - - - - - - - - - - - - - - - - -aaatataa