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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttctttttataactaactatgtttttcaaacttattctctcttccttccgttaataactttgtttatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCCCACGATGACATCAAAACTCTCGCTGGTGGCAGCGTTGCCAACACAATTC

Basic information

species Glycine max
transcript GLYMA04G03290.1
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|208088262|gb|GD889430.1|GD889430
EST:     TCGCATTCCCGGCGAGCGCGGTAGGACTCCAATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATC
genomic: TCGCATTCCCGGCGAGCGCGGT-GG-CTCC-ATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATC
EST: gi|298196538|gb|HO041281.1|HO041281
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|6481426|gb|AW200697.1|AW200697
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|208330065|gb|GE127642.1|GE127642
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGA-CTGGAATCCATA
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATA
EST: gi|15814578|gb|BI786853.1|BI786853
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|15200940|gb|BI424609.1|BI424609
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|192334033|gb|FK026190.1|FK026190
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|298173637|gb|HO016973.1|HO016973
EST:     TTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: TTGGTCCTTGCTCCATCGCATTCCCGGCGAGCG-CGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|209706384|gb|BW670787.1|BW670787
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|298179451|gb|HO027922.1|HO027922
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|16348682|gb|BI974268.1|BI974268
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|298186858|gb|HO033957.1|HO033957
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|192323065|gb|FK016316.1|FK016316
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|192326921|gb|FK015148.1|FK015148
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|16996508|gb|BM085880.1|BM085880
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|298173676|gb|HO017012.1|HO017012
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|41145774|gb|CK605985.1|CK605985
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|208174723|gb|GD967746.1|GD967746
EST:     TCCATCGCATTTCCCGGCGTAGTCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: TCCATCGCA-TTCCCGGCG-AG-CGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|298185496|gb|HO030709.1|HO030709
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
EST: gi|7691339|gb|AW759397.1|AW759397
EST:     ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCT                         GTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC
genomic: ATTGGTCCTTGCTCCATCGCATTCCCGGCGAGCGCGGTGGCTCCATCCCTgtctgttctt ... tatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttcaaacttattctctcttccttccgttaataactttgtttatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCCCACGATGACATCAAAACTCTCGCTGGTGGCAGCGTTGCCAACACAATTC
                                taataac  putative branch site (score: 1)
                                      ctttgttt  CT-rich tract
                               ttaataactttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgttctttttataactaactatgtttttcaaacttattctctcttccttccgttaataactttgtttatcctacagGTCCAAATTGAAGAACTGGAATCCATACTGAGAGAGGTTAAATCCAAATCCCACGATGACATCAAAACTCTCGCTGGTGGCAGCGTTGCCAACACAATTC

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