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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaatgatttgtttgtagtcagttaagtgaagaattaatttataatgcagtaatgactaatacaagaatatttttcttctcctttttgttccctgcaggAGCCAAGAGTCATGTCCAAGCTCCAAGAAGAGG

Basic information

species Glycine max
transcript GLYMA18G47500.2
intron # 5
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|7588838|gb|AW704625.1|AW704625
EST:     TGAAACATCAGCTGCTGTTTTAACTTGGACCTTTTATCTTCTATCCAAGG                         AGCCAAGAGTCATGTCCAAGCTCCAAGAAGAGG
genomic: TGAAACATCAGCTGCTGTTTTAACTTGGACCTTTTATCTTCTATCCAAGGtaataattcg ... tccctgcaggAGCCAAGAGTCATGTCCAAGCTCCAAGAAGAGG
EST: gi|15286273|gb|BI470164.1|BI470164
EST:     TGAAACATCAGCTGCTGTTTTAACTTGGACCTTTTATCTTCTATCCAAGG                         AGCCAAGAGTCATGTCCAAGCTCCAAGAAGAGG
genomic: TGAAACATCAGCTGCTGTTTTAACTTGGACCTTTTATCTTCTATCCAAGGtaataattcg ... tccctgcaggAGCCAAGAGTCATGTCCAAGCTCCAAGAAGAGG
EST: gi|7588874|gb|AW704660.1|AW704660
EST:     TGAAACATCAGCTGCTGTTTTAACTTGGACCTTTTATCTTCTATCCAAGG                         AGCCAAGAGTCATGTCCAAGCTCCAAGAAGAGG
genomic: TGAAACATCAGCTGCTGTTTTAACTTGGACCTTTTATCTTCTATCCAAGGtaataattcg ... tccctgcaggAGCCAAGAGTCATGTCCAAGCTCCAAGAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcagtaatgactaatacaagaatatttttcttctcctttttgttccctgcaggAGCCAAGAGTCATGTCCAAGCTCCAAGAAGAGG
          gactaat  putative branch site (score: 2)
                        tatttttcttctcctt  putative PPT
             taatacaagaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaatgatttgtttgtagtcagttaagtgaagaattaatttataatgcagtaatgactaatacaagaatatttttcttctcctttttgttccctgcaggAGCCAAGAGTCATGTCCAAGCTCCAAGAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - tgcagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatacaag