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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttgcaaaatttgtaccctggttcgagtaatttaatgccattgagatatatcttgatgaaagataacagtggtttctaagcttattgttctttatcagAGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTGATGGGAAAGCTACGGAGATAACCAAAATTAGCCCTGTTGGTGGGGGTTG

Basic information

species Glycine max
transcript GLYMA03G01960.1
intron # 1
splice site 3'
intron type U2

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|192313607|gb|FK007283.1|FK007283
EST:     ACTTCCTCGACTTCTTCGACCTTCTTTCACCAAAACCAAATCATCACCTA                         AGTTCAGCATGAGCATGAGCAAGGATCCAGTTCGTGAGTGGATTCTTTCTG
genomic: ACTTCCTCGACTTCTTCGACCTTCTTTCACCAAAACCAAATCATCACCTAgtaagttaac ... tctttatcagAGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTG
EST: gi|192318364|gb|FK007282.1|FK007282
EST:     ACTTCCTCGACTTCTTCGACCTTCTTTCACCAAAACCAAATCATCACCTA                         AGTTCAGCATGAGCATGAGCAAGGATCCAGTTCGTGAGTGGATTCTTTCTG
genomic: ACTTCCTCGACTTCTTCGACCTTCTTTCACCAAAACCAAATCATCACCTAgtaagttaac ... tctttatcagAGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTG
EST: gi|298191837|gb|HO035919.1|HO035919
EST:     ACTTCCTCGACTTCTTCGACCTTCTTTCACCAAAACCAAATCATCACCTA                         AGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTG
genomic: ACTTCCTCGACTTCTTCGACCTTCTTTCACCAAAACCAAATCATCACCTAgtaagttaac ... tctttatcagAGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTG
EST: gi|209708526|gb|BW668137.1|BW668137
EST:     ACTTCCTCGACTTCTTCGACCTTCTTTCACCAAAACCAAATCATCACCTA                         AGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTG
genomic: ACTTCCTCGACTTCTTCGACCTTCTTTCACCAAAACCAAATCATCACCTAgtaagttaac ... tctttatcagAGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTG
EST: gi|120496729|gb|EH224896.1|EH224896
EST:     CTTCGACCTTCTTTCA-CAAAACCAAATCATCACCTA                         AGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTG
genomic: CTTCGACCTTCTTTCACCAAAACCAAATCATCACCTAgtaagttaac ... tctttatcagAGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTG
EST: gi|6133930|gb|AW132323.1|AW132323
EST:     ACTTCCTCGACTTCTTCGACCTTCTTTCACCAAAACCAAATCATCACCTA                         AGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTG
genomic: ACTTCCTCGACTTCTTCGACCTTCTTTCACCAAAACCAAATCATCACCTAgtaagttaac ... tctttatcagAGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTG
EST: gi|298164909|gb|HO010906.1|HO010906
EST:     ACTTCCTCGACTTCTTCGACCTTCTTTCACCAAAACCAAATCATCACCTA                         AGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTG
genomic: ACTTCCTCGACTTCTTCGACCTTCTTTCACCAAAACCAAATCATCACCTAgtaagttaac ... tctttatcagAGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatatatcttgatgaaagataacagtggtttctaagcttattgttctttatcagAGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTGATGGGAAAGCTACGGAGATAACCAAAATTAGCCCTGTTGGTGGGGGTTG
                 agataac  putative branch site (score: 3)
                                         ttgttcttt  putative PPT
                                      ttattgttctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actttgcaaaatttgtaccctggttcgagtaatttaatgccattgagatatatcttgatgaaagataacagtggtttctaagcttattgttctttatcagAGTTCAGCATGAGCATGAGCAAGGATCCGGTTCGTGAGTGGATTCTTTCTGATGGGAAAGCTACGGAGATAACCAAAATTAGCCCTGTTGGTGGGGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
-ctttgca
- - - - - - - - - -ctggttc
- - - - - - - - - - - - - - - - - -aatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - -cttgatg