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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attagattaattatcactgaatgaatcatattgcactggtgattggatccacatttatttgttatttcatcttcagacctaagttgtgagttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT

Basic information

species Glycine max
transcript GLYMA04G36600.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G36600.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 3'ss of exon 4
attagattaattatcac--tgaatgaatcatattgcactggtgat--tggatccacatttatttgttatttcatcttcagacctaagttgtgagttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT
  |  | || || ||||  |   | |||  || | || || ||||  | | |    | || | ||  |  |      || |  || | | |||  ||| |  |||| || |||||||| ||||  || ||||| |||||  | ||||||||||| |  |||||||| ||||| |||||||| |||||||| |||||||| 
-atgtactatttttcacactttttaaatagtagtaca-tgttgatagtagctgtgaacttgtatgccagatagctcacatatttatgct-tga-ctgaatgcagGTTTCGGCAATAGTTTCATGTTTACTGGGCCCTGATCGTGCAGAAAAAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCA

upper sequence: GLYMA04G36600.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G48420.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------------------------------------attagattaattatcactgaatgaatcatattgcactggtgattggatccacattta-------tttgttatttcatcttcagacctaagttgtgagttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT
                                                                                      |  ||| ||       ||| ||   | | ||     ||         ||     |||       | | | ||   |  | |    || | || |    |||||| |||| ||||| ||||| |||| |||||| ||||| ||  ||||||| |||||||||||||| ||||||||||| || |||   || || |||||||| 
gtatgatcaatcaggttctactacttcagtttcctgagaccataaccatatatctcaaaatcttgtatcctgatgagttttcgtaaacaagactacgcgcagctgcatcgttaacatgaatatgcgagcatcgtcttagcttagaagaactgtataatcggaaatacttttctcatttcttgcctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA

upper sequence: GLYMA04G36600.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 3'ss of exon 4
attagattaattatca-ctgaatgaatcatattgcactggtgattggatccacatttatttgttatttcatcttcagacctaagttgtgagttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT
  | | ||  | ||   |||| |   |          || |  | |  | |  || || || | ||||      | ||  ||  | |||     ||   |||||||||||||||| |||| ||||||||| |||||| |||||||||||||||||||||||||||| ||||||||||| || |||||||||||||| 
tcttgctttgtcattgtctgatttccttggcgaattatgatattggttttctgatctaattctcattttgataactgaattatat-gtgctaatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATCAAGATATTTGCAGGCGACGTGGTTCCTCGAAAAAAGCCTGATCCA

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|120495078|gb|EH223245.1|EH223245
EST:     TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCG                         GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
genomic: TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCGgtatgcataa ... ttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
EST: gi|8670194|gb|BE191301.1|BE191301
EST:     TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCG                         GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
genomic: TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCGgtatgcataa ... ttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
EST: gi|20811539|gb|BQ296017.1|BQ296017
EST:     TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCG                         GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
genomic: TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCGgtatgcataa ... ttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
EST: gi|9258673|gb|BE346820.1|BE346820
EST:     TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCG                         GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
genomic: TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCGgtatgcataa ... ttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
EST: gi|209718041|gb|BW671874.1|BW671874
EST:     GTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCG                         GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
genomic: GTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCGgtatgcataa ... ttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
EST: gi|19269931|gb|BM886187.1|BM886187
EST:     TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCG                         GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
genomic: TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCGgtatgcataa ... ttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
EST: gi|192318370|gb|FK011026.1|FK011026
EST:     TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCG                         GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGNNNNNNNT
genomic: TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCGgtatgcataa ... ttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAG-AAAAAAT
EST: gi|6718650|gb|AW306297.1|AW306297
EST:     CCAACGAGAAGGCG                         GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
genomic: CCAACGAGAAGGCGgtatgcataa ... ttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
EST: gi|9564563|gb|BE474072.1|BE474072
EST:     TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCG                         GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC
genomic: TTGCTCAAGGAGTCCAAGTTGCAGTTTGCAGCACTTCCAACGAGAAGGCGgtatgcataa ... ttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatccacatttatttgttatttcatcttcagacctaagttgtgagttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT
                                           agttgat  putative branch site (score: 5)
       atttatttgttatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attagattaattatcactgaatgaatcatattgcactggtgattggatccacatttatttgttatttcatcttcagacctaagttgtgagttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - cactgaa
- - - - - - - - - - - - - - - -tgcactg
- - - - - - - - - - - - - - - - - - - gtgattg
- - - - - - - - - - - - - - - - - - - - - - - atccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agttgtg