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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacatggccatgttggagtatgatattcatggtttatgcttcacttaactgatgaatttgtgctgatggctgtaattttttcttcttcaaaatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCGGAAGGGAATAGCTAAACACTTGGTTGCAAAGGCAGAATCACAAGCTAGA

Basic information

species Glycine max
transcript GLYMA20G32020.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32020.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0019g04360.t01 (Vitis vinifera), 3'ss of exon 2
---tacatggccatgttggagtatgatattcatggtttatgcttcactta--actgatgaatttgtgctgatggctgtaattttttcttcttcaaaatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCGGAAGGGAATAGCTAAACACTTGGTTGCAAAGGCAGAATCACAAGCTAGA
| || | || | || | | ||| ||| ||| |||||| | |||| |||| || || || || | || |||| ||||||||| |||||||||||||| ||||| || || | ||| ||||| ||||| ||||| ||| | | | ||||||||| | |||||||||
ggatgcacaattgtagaagatatgaacctttaacttgtatacttacattactactgattattttgctctgacaagtgaggcattgattttatc-----attgcagGAGTGGAATTGCTTACATATCAAATGTTGCAGTTCGGGAGACATTCAGGCGCAAGGGGATAGCCAAAAGGCTTATAGTAAAGGCAGAGGCTCAAGCTAGA
















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|193579894|gb|FK533541.1|FK533541
EST:     TTGCGACAGAGAAG                         GACTGGAATTGCATACATATCAAATGTGGCAGTCCGAG-AAAATTTAGGCG
genomic: TTGCGACAGAGAAGgtgagttgaa ... aatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCG
EST: gi|193540177|gb|FK495647.1|FK495647
EST:     AGGGACCATTGCGACAGAGAAG                         GACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCG
genomic: AGGGACCATTGCGACAGAGAAGgtgagttgaa ... aatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCG
EST: gi|207807782|gb|GD778131.1|GD778131
EST:     GATACTGTTGCAGACTTTCTGCCTAGGAAGGGACCATTGCGACAGAGAAG                         GACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTA
genomic: GATACTGTTGCAGACTTTCTGCCTAGGAAGGGACCATTGCGACAGAGAAGgtgagttgaa ... aatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTA
EST: gi|208126091|gb|GD926035.1|GD926035
EST:     GATACTGTTGCAGACTTTCTGCCTAGGAAGGGACCATTGCGACAGAGAAG                         GACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCG
genomic: GATACTGTTGCAGACTTTCTGCCTAGGAAGGGACCATTGCGACAGAGAAGgtgagttgaa ... aatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCG
EST: gi|193677454|gb|FK619668.1|FK619668
EST:     TTGCGACAGAGAAG                         GACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCG
genomic: TTGCGACAGAGAAGgtgagttgaa ... aatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCG
EST: gi|213602030|gb|DB976249.1|DB976249
EST:     ATACTGTTGCAGAC-TTCATGCCTAGGAAGGGACCATTGCGACAGAGAAG                         GACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCG
genomic: ATACTGTTGCAGACTTTC-TGCCTAGGAAGGGACCATTGCGACAGAGAAGgtgagttgaa ... aatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCG
EST: gi|193317855|gb|FK284593.1|FK284593
EST:     ATACTGTTGCAGACTTTCTGCCTAGGAAGGGGACCATTGCGACAGAGAAG                         GACTGGAATTGCATACATATCAAATGTGGCAGTCCGAG-AAAATTTAGGCG
genomic: ATACTGTTGCAGACTTTCTGCCTAGGAA-GGGACCATTGCGACAGAGAAGgtgagttgaa ... aatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCG
EST: gi|193582689|gb|FK536041.1|FK536041
EST:     TTGCGACAGAGAAG                         GACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCG
genomic: TTGCGACAGAGAAGgtgagttgaa ... aatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCG
EST: gi|193657670|gb|FK607213.1|FK607213
EST:     TTGCGACAGAGAAG                         GTACTTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGG
genomic: TTGCGACAGAGAAGgtgagttgaa ... aatactgtagG-AC-TGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGG
EST: gi|208166231|gb|GD965465.1|GD965465
EST:     GATACTGTTGCAGACTTTCTGCCTAGGAAGGGACCATTGCGACAGAGAAG                         GACTGGAATTGCA
genomic: GATACTGTTGCAGACTTTCTGCCTAGGAAGGGACCATTGCGACAGAGAAGgtgagttgaa ... aatactgtagGACTGGAATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactgatgaatttgtgctgatggctgtaattttttcttcttcaaaatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCGGAAGGGAATAGCTAAACACTTGGTTGCAAAGGCAGAATCACAAGCTAGA
               tgctgat  putative branch site (score: 3)
 taattttttcttcttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacatggccatgttggagtatgatattcatggtttatgcttcacttaactgatgaatttgtgctgatggctgtaattttttcttcttcaaaatactgtagGACTGGAATTGCATACATATCAAATGTGGCAGTCCGAGAAAAATTTAGGCGGAAGGGAATAGCTAAACACTTGGTTGCAAAGGCAGAATCACAAGCTAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT