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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaacgatgcttctcttttccttacacaaaattctgtttctgttctttttttattttattttaacaatctaaattggagaggaaatttatggtggcatttgtgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCATTCTGAAGCACTTGGGAATAAGGGAATACTTCTCGGAGATTAACACTAAC

Basic information

species Glycine max
transcript GLYMA08G20820.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20820.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G73010.1 (Arabidopsis thaliana), 3'ss of exon 2
--------gtatgtaacgatgcttctc---ttttccttaca----caaaattctgtttctgttc---tttttttattttattttaaca-atctaa-attggagaggaa-----atttatggt--ggcatttgtgtgtt-----tcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCATTCTGAAGCACTTGGGAATAAGGGAATACTTCTCGGAGATTAACACTAAC
         |   | |  || |||      ||||  ||  |      ||||| |   | | |     | ||||| || ||||  || |  |||||  || || |  |      |||| || |  |  ||||  | |||     ||||||||||  | ||||| ||||| |||||||||||||||||||| ||||||||  |  | ||  | ||||| || |||  |||||| ||||| ||| | |||
gtaataatcttcattattattctttctagtttttgtttgtaactatcaaattttacatgtctaacaatattttttttctattaaaatatgtctaatgttagacaaaacccaccatttctgatccgatatttacgggttcggtttcagGTGTGAGCTTAGGATAGTGAGCGATGCAAACATGTTTTTCATCGAGACCATCGTTGAACATCTCGGAATTAGCGAACTCTTCTCTGAGATCAACTCGAAC
















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|192304348|gb|FG996460.1|FG996460
EST:     CTTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|9258334|gb|BE346481.1|BE346481
EST:     CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|192294661|gb|FG986510.1|FG986510
EST:     CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|51338133|gb|CO981999.1|CO981999
EST:     CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|9259860|gb|BE348007.1|BE348007
EST:     CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|5770626|gb|AI973800.1|AI973800
EST:     CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|8670193|gb|BE191300.1|BE191300
EST:     CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|298176773|gb|HO023246.1|HO023246
EST:     CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|9205184|gb|BE331408.1|BE331408
EST:     CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|9258289|gb|BE346436.1|BE346436
EST:     CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|298196445|gb|HO041188.1|HO041188
EST:     CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|7638852|gb|AW733245.1|AW733245
EST:     CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|9204888|gb|BE331112.1|BE331112
EST:     CCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
EST: gi|209709143|gb|BW683990.1|BW683990
EST:     CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGG                         GTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT
genomic: CCTTTGCACCCAAGAGTAATACCCGCTATTCAAGCAGCTCATGCTTTCGGgtatgtaacg ... tgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttaacaatctaaattggagaggaaatttatggtggcatttgtgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCATTCTGAAGCACTTGGGAATAAGGGAATACTTCTCGGAGATTAACACTAAC
     taacaatctaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaacgatgcttctcttttccttacacaaaattctgtttctgttctttttttattttattttaacaatctaaattggagaggaaatttatggtggcatttgtgtgtttcagGTGTGATTTGAGGATTGTGAGTGATGCAAACATGTTTTTCATTGAGACCATTCTGAAGCACTTGGGAATAAGGGAATACTTCTCGGAGATTAACACTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT