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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaggaaactaatctaacttttttacttgctagattgagattatgaatagtattgctattgcattaatttacattgcaacttctccttttggactccagACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGAGAAGGGGAGGAAAACAAAGATGCTTCGGCTACTGCCGATCTCCTCGAGAA

Basic information

species Glycine max
transcript GLYMA01G29410.1
intron # 3
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|298173186|gb|HO020170.1|HO020170
EST:     TGGGGAATTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGA                         ACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGAG
genomic: TGGGGAATTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGAgtgagtctct ... tggactccagACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGAG
EST: gi|298164310|gb|HO013955.1|HO013955
EST:     TGGGGAATTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGA                         ACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGA
genomic: TGGGGAATTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGAgtgagtctct ... tggactccagACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGA
EST: gi|213614876|gb|DB956984.1|DB956984
EST:     TGGGGAATTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGA                         ACTGTAAGGCCTTCATGACAACTATGNCA-GAAGTGGCAGAATCACAAGGA
genomic: TGGGGAATTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGAgtgagtctct ... tggactccagACTGTAAGGCCTTCATGACAACTATG-CAAGAAGTGGCAGAATCACAAGGA
EST: gi|207773285|gb|GD743191.1|GD743191
EST:     TTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGA                         ACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGAG
genomic: TTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGAgtgagtctct ... tggactccagACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGAG
EST: gi|207831820|gb|GD804324.1|GD804324
EST:     TGGGGAATTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGA                         ACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGAG
genomic: TGGGGAATTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGAgtgagtctct ... tggactccagACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGAG
EST: gi|213592588|gb|DB961848.1|DB961848
EST:     TGGGGAATTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGA                         ACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGAG
genomic: TGGGGAATTGAAGGATGAGCTGTTCTGTATTAGGTTTCCCTCTGTTGAGAgtgagtctct ... tggactccagACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatagtattgctattgcattaatttacattgcaacttctccttttggactccagACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGAGAAGGGGAGGAAAACAAAGATGCTTCGGCTACTGCCGATCTCCTCGAGAA
                 cattaat  putative branch site (score: 3)
                                caacttctcctttt  putative PPT
            tattgcattaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtaggaaactaatctaacttttttacttgctagattgagattatgaatagtattgctattgcattaatttacattgcaacttctccttttggactccagACTGTAAGGCCTTCATGACAACTATGCAAGAAGTGGCAGAATCACAAGGAGAAGGGGAGGAAAACAAAGATGCTTCGGCTACTGCCGATCTCCTCGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - -gaaactaa
- - - - - - - - - - - - tacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattgca