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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatcgaacgaactttttactgatgaagcaaggatatattttccatgatttttaaaattgcttaatttaattcatgtacaactaagaatgtttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT

Basic information

species Glycine max
transcript GLYMA04G39930.2
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|15337599|gb|BI498255.1|BI498255
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAA-TCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298183638|gb|HO028851.1|HO028851
EST:     TTCCTCCGCCGTCGTTAAGCTCCTGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTGAA
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTGAA
EST: gi|4313704|gb|AI460823.1|AI460823
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGGAAAATCTAGCTTCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|10233755|gb|BE802643.1|BE802643
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298197610|gb|HO045089.1|HO045089
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|20076003|gb|BQ094786.1|BQ094786
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|18692743|gb|BM521591.1|BM521591
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|6070236|gb|AW099772.1|AW099772
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|16347621|gb|BI973216.1|BI973216
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298173808|gb|HO017144.1|HO017144
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGCCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298181231|gb|HO022670.1|HO022670
EST:     TTCCTCCTCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|213608229|gb|DB970826.1|DB970826
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298165022|gb|HO011071.1|HO011071
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|23730997|gb|BU763608.1|BU763608
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298173236|gb|HO020220.1|HO020220
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|19347357|gb|BM892237.1|BM892237
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|7685971|gb|AW756619.1|AW756619
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298174724|gb|HO014755.1|HO014755
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGCTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298183088|gb|HO028351.1|HO028351
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298166785|gb|HO010224.1|HO010224
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|120532869|gb|EH261002.1|EH261002
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|8826470|gb|BE210200.1|BE210200
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298191328|gb|HO038807.1|HO038807
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298164553|gb|HO014198.1|HO014198
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|213617768|gb|DB959380.1|DB959380
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298195572|gb|HO043963.1|HO043963
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|209696790|gb|BW680411.1|BW680411
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|213587591|gb|DB969732.1|DB969732
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|298185168|gb|HO030381.1|HO030381
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|6566815|gb|AW234447.1|AW234447
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
EST: gi|4313692|gb|AI460811.1|AI460811
EST:     TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAG                         GTCACGTCAACCATTCTANTTTCTGGAAAAATCTAGCTCCTGTTCGT
genomic: TTCCTCCGCCGTCGTTAAGCTCCAGGGCGCCATCAAGTTCAACGGCGGAGgtccgattcc ... tttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttttaaaattgcttaatttaattcatgtacaactaagaatgtttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT
                   atttaat  putative branch site (score: 4)
     tttaaaattgcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatcgaacgaactttttactgatgaagcaaggatatattttccatgatttttaaaattgcttaatttaattcatgtacaactaagaatgtttattgcagGTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT

- - - - - - - - - actgatg
- - - - - - - - - - - - - - - - - - - - -tccatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtac