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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagttaaaatgtctattttatcttggtctgtttgcctttcactttgcatcacgccttcacccatttgagcaacttcctgataaatatgtagtatacttatgtagtaacctgttaaaacaaaatgcagGAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATAATTGTTACTACCATTGGTGGTAAAAATGGCCAGCCAAAGCAG

Basic information

species Glycine max
transcript GLYMA02G01220.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01220.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 2
gtaaagttaaaatgtctattttatcttggtctgtttgcctttcactttgcatcacgccttcacccatttgagcaacttcctgataaatatgtagtatacttatgtagtaacctgttaaaacaaaatgcagGAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATAATTGTTACTACCATTGGTGGTAAAAATGGCCAGCCAAAGCAG
||| | || | |||||| ||| ||| | || ||| |||| || ||| | | | || |||| | | || |||||||||||| |||||||| ||||| |||||||| || || || ||||||||||| || || ||||| || |||||||||||||||||||||
-------------------------gtggatcatgtggttc---ctttgcttcattttttcttcttcttct----ctttttgatttat-tgttgggccatctta----aatctgtcttgatatcttgtagGAAATGGAAGATACTGTGGTGGATGGTAATGGGACAGAGACTGGTCATATAATTGTAACAACTATTGGAGGGAAAAATGGCCAGCCAAAGCAG
















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|208319851|gb|GE114614.1|GE114614
EST:     AAAGGTTGCCTGATGAGATGAATAGGACAATGAAAATTAGGGATGAAAGG                         GAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATA
genomic: AAAGGTTGCCTGATGAGATGAAT-GG-C-ATGAAAATTAGGGATGAAAGGgtaaagttaa ... caaaatgcagGAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATA
EST: gi|120532325|gb|EH260458.1|EH260458
EST:     TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGG                         GAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATA
genomic: TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGGgtaaagttaa ... caaaatgcagGAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATA
EST: gi|193488973|gb|FK456670.1|FK456670
EST:     TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGG                         GAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATA
genomic: TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGGgtaaagttaa ... caaaatgcagGAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATA
EST: gi|193329498|gb|FK296064.1|FK296064
EST:     TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGG                         GAAATGGAAGCAACTAGTGGTAGATGGAAATGGGACTGAAACAGGACATAT
genomic: TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGGgtaaagttaa ... caaaatgcagGAAATGGAAGCAACT-GTGGTAGATGGAAATGGGACTGAAACAGGACATAT
EST: gi|193586534|gb|FK538560.1|FK538560
EST:     TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGG                         GAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACGTATA
genomic: TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGGgtaaagttaa ... caaaatgcagGAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATA
EST: gi|208229998|gb|GE023381.1|GE023381
EST:     TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGG                         GAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGA
genomic: TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGGgtaaagttaa ... caaaatgcagGAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGA
EST: gi|193632426|gb|FK583774.1|FK583774
EST:     TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGG                         GAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATA
genomic: TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGGgtaaagttaa ... caaaatgcagGAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATA
EST: gi|193577033|gb|FK535206.1|FK535206
EST:     TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGG                         GAAATGGAAGCAACTGT
genomic: TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGGgtaaagttaa ... caaaatgcagGAAATGGAAGCAACTGT
EST: gi|193356257|gb|FK321430.1|FK321430
EST:     TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGG                         GAA-TGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATA
genomic: TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGGgtaaagttaa ... caaaatgcagGAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATA
EST: gi|207797139|gb|GD771147.1|GD771147
EST:     TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGG                         GAAATGGAAGCAAACTAGTGGTAGATGGAAATGGGA
genomic: TTGAAAGGTTGCCTGATGAGATGAATGGCATGAAAATTAGGGATGAAAGGgtaaagttaa ... caaaatgcagGAAATGGAAGCAA-CT-GTGGTAGATGGAAATGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcctgataaatatgtagtatacttatgtagtaacctgttaaaacaaaatgcagGAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATAATTGTTACTACCATTGGTGGTAAAAATGGCCAGCCAAAGCAG
                             tagtaac  putative branch site (score: 1)
 ataaatatgtagtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagttaaaatgtctattttatcttggtctgtttgcctttcactttgcatcacgccttcacccatttgagcaacttcctgataaatatgtagtatacttatgtagtaacctgttaaaacaaaatgcagGAAATGGAAGCAACTGTGGTAGATGGAAATGGGACTGAAACAGGACATATAATTGTTACTACCATTGGTGGTAAAAATGGCCAGCCAAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG