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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatcttattgctttgtttcttgtgtgcatcagtttatatgctttattcacgtgatatttctgtcccgttattactgacatgtgctaattattataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAATGACAACAAGAGGACTTGGTGAGAAAGAATTTTCACTCATTGCTGATTT

Basic information

species Glycine max
transcript GLYMA13G29410.2
intron # 9
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|209700551|gb|BW670390.1|BW670390
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|209725263|gb|BW672738.1|BW672738
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|20075616|gb|BQ094399.1|BQ094399
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|213606991|gb|DB974384.1|DB974384
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|18038805|gb|BM307099.1|BM307099
EST:     CTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: CTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|213603861|gb|DB982161.1|DB982161
EST:     AAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCAACAGCAA
genomic: AAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|213593328|gb|DB975696.1|DB975696
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|193514366|gb|FK467896.1|FK467896
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|209725542|gb|BW677842.1|BW677842
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|209710250|gb|BW681112.1|BW681112
EST:     CCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: CCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|37995170|gb|CF806759.1|CF806759
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|15286064|gb|BI469955.1|BI469955
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|214004065|gb|DB984971.1|DB984971
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|213594045|gb|DB983197.1|DB983197
EST:     TGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCAACAGCAA
genomic: TGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|209727332|gb|BW651586.1|BW651586
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|19052654|gb|BM731321.1|BM731321
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|214008826|gb|DB988277.1|DB988277
EST:     AAAATTCTTGAC-TGCGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: AAAATTCTTGACTTG-GCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|6454780|gb|AW185463.1|AW185463
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
EST: gi|302141299|gb|HO212175.1|HO212175
EST:     GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTG                         GTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA
genomic: GAAAATTCTTGACTTGGCTTCTATAACCCTCAACAAAAATTCAGTGCCTGgtgagatctt ... attataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcacgtgatatttctgtcccgttattactgacatgtgctaattattataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAATGACAACAAGAGGACTTGGTGAGAAAGAATTTTCACTCATTGCTGATTT
                                     tgctaattattataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatcttattgctttgtttcttgtgtgcatcagtttatatgctttattcacgtgatatttctgtcccgttattactgacatgtgctaattattataaaagGTGATAAGAGTGCCCTAGTTCCAGGAGGCATTCGCATTGGGGCACCAGCAATGACAACAAGAGGACTTGGTGAGAAAGAATTTTCACTCATTGCTGATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT