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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatgagttaactattgctatactatgtgttccttcatcctctactccatattgtcattgcatgtttgatttgtaaaacattcctgtgttaccagAAACCTCCTGAGCTTGATGCTCCTCTCCTCGAGACAACTGAAGGAGGAGAAAAGGAAGCCAAATTTGAAAATCAAGTGCAAGAGGACATGAACGTCTTCT

Basic information

species Glycine max
transcript GLYMA12G07890.2
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G07890.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 22
gtaacatgagttaac-tattgctatactatgtgttccttcatcctctac-tccat--attgtcat--tgcatgtttgatttgtaaaacattcct-gtgttaccagAAACCTCCTGAGCTTGATGCTCCTCTCCTCGAGACAACTGAAGGAGGAGAAAAGGAAGCCAAATTTGAAAATCAAGTGCAAGAGGAC--ATGAACGTCTTCT-
     || || || | ||  ||||||  |  || |  |   | || | | | |||  ||||| ||  |    |||| ||   ||  | |||| |    ||  ||||| |||||||||||||||||||||| | | ||||||||||| |  |   |||||||||  |||| ||   |||  |  |    |||   |  |||   |  | 
-----attagatatcctagagctatataagatgatgttctctacttttcatgcatgaattgttatattctgggtttaatgactactatattcatcaaatttgcagAACCCTCCTGAGCTTGATGCTCCTCCCTTGGAGACAACTGATGCTG---AAAAGGAAGTTAAATCTGTGGATCCTGAACTCCTGGATCTACAAACAAATATTT
















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|51337410|gb|CO981276.1|CO981276
EST:     AGAACCATCCGTTCTTTCGGGGTGTCAATTGGGCCCTAGTTCGTTGCACG                         AAACCTCCTGAGCTTGATGCTCCTCTCCTCGAGACAACTGAAGGAGGAGAA
genomic: AGAACCATCCGTTCTTTCGGGGTGTCAATTGGGCCCTAGTTCGTTGCACGgtaacatgag ... gtgttaccagAAACCTCCTGAGCTTGATGCTCCTCTCCTCGAGACAACTGAAGGAGGAGAA
EST: gi|151393210|gb|EV263085.1|EV263085
EST:     AGAACCATCCGTTCTTTCGGGGTGTCAATTGGGCCCTAGTTCGTTGCACG                         AAACCTCCTGAGCTTGATGCTCCTCTCCTCGAGACAACTGAAGGAGGAGAA
genomic: AGAACCATCCGTTCTTTCGGGGTGTCAATTGGGCCCTAGTTCGTTGCACGgtaacatgag ... gtgttaccagAAACCTCCTGAGCTTGATGCTCCTCTCCTCGAGACAACTGAAGGAGGAGAA
EST: gi|31475124|gb|CD417152.1|CD417152
EST:     AGAACCATCCGTTCTTTCGGGGTGTCAATTGGGCCCTAGTTCGTTGCACG                         AAACCTCCTGAGCTTGATGCTCCTCTCCTCGAGACAACTGAAGGAGGAGAA
genomic: AGAACCATCCGTTCTTTCGGGGTGTCAATTGGGCCCTAGTTCGTTGCACGgtaacatgag ... gtgttaccagAAACCTCCTGAGCTTGATGCTCCTCTCCTCGAGACAACTGAAGGAGGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctactccatattgtcattgcatgtttgatttgtaaaacattcctgtgttaccagAAACCTCCTGAGCTTGATGCTCCTCTCCTCGAGACAACTGAAGGAGGAGAAAAGGAAGCCAAATTTGAAAATCAAGTGCAAGAGGACATGAACGTCTTCT
                       gtttgat  putative branch site (score: 5)
                                        ttcctgt  putative PPT
                        tttgatttgtaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatgagttaactattgctatactatgtgttccttcatcctctactccatattgtcattgcatgtttgatttgtaaaacattcctgtgttaccagAAACCTCCTGAGCTTGATGCTCCTCTCCTCGAGACAACTGAAGGAGGAGAAAAGGAAGCCAAATTTGAAAATCAAGTGCAAGAGGACATGAACGTCTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA