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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcttgtatccttgtgttaatctgtctatagttagtatccattagttatttgactctttctagcttacatttgtaatctacaaatgtttgcttattcagTGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGAGGGAAGGGAAAGGGGAAACAGGCTGCAAGTGGAAGTGATGAGAATGCTT

Basic information

species Glycine max
transcript GLYMA04G33180.2
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|298180788|gb|HO022227.1|HO022227
EST:     TCCACTGAGGTGACTCGTCGCGCTTTACAAATTCTCAGTCTGCGACTCTG                         TGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
genomic: TCCACTGAGGTGACTCGTCGCGCTTTACAAATTCTCAGTCTGCGACTCTGgtatgtatgc ... gcttattcagTGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
EST: gi|192310835|gb|FK000321.1|FK000321
EST:     TCCACTGAGGTGACTCGTCGCGCTTTACAAATTCTCAGTCTGCGACTCTG                         TGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
genomic: TCCACTGAGGTGACTCGTCGCGCTTTACAAATTCTCAGTCTGCGACTCTGgtatgtatgc ... gcttattcagTGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
EST: gi|209720765|gb|BW677555.1|BW677555
EST:     GTCGTGCTTTACAAATTCTCAGTCTGCGACTCTG                         TGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
genomic: GTCGCGCTTTACAAATTCTCAGTCTGCGACTCTGgtatgtatgc ... gcttattcagTGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
EST: gi|298165798|gb|HO008769.1|HO008769
EST:     TCCACTGAGGTGACTCGTCGCGCTTTACAAATTCTCAGTCTGCGACTCTG                         TGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
genomic: TCCACTGAGGTGACTCGTCGCGCTTTACAAATTCTCAGTCTGCGACTCTGgtatgtatgc ... gcttattcagTGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
EST: gi|298182306|gb|HO026481.1|HO026481
EST:     GTCGCGCTTTACAAATTCTCAGTCTGCGACTCTG                         TGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
genomic: GTCGCGCTTTACAAATTCTCAGTCTGCGACTCTGgtatgtatgc ... gcttattcagTGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
EST: gi|298168618|gb|HO009548.1|HO009548
EST:     TCCACTGAGGTGACTCGTCGCGCTTTACAAATTCTCAGTCTGCGACTCTG                         TGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
genomic: TCCACTGAGGTGACTCGTCGCGCTTTACAAATTCTCAGTCTGCGACTCTGgtatgtatgc ... gcttattcagTGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
EST: gi|27423863|gb|CA935383.1|CA935383
EST:     CGCGCTTTACAAATTCTCAGTCTGCGACTCTG                         TGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
genomic: CGCGCTTTACAAATTCTCAGTCTGCGACTCTGgtatgtatgc ... gcttattcagTGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
EST: gi|41145676|gb|CK605887.1|CK605887
EST:     GCGCTTTACAAATTCTCAGTCTGCGACTCTG                         TGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA
genomic: GCGCTTTACAAATTCTCAGTCTGCGACTCTGgtatgtatgc ... gcttattcagTGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatttgactctttctagcttacatttgtaatctacaaatgtttgcttattcagTGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGAGGGAAGGGAAAGGGGAAACAGGCTGCAAGTGGAAGTGATGAGAATGCTT
                 agcttac  putative branch site (score: 3)
                                          tttgctt  putative PPT
                        atttgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcttgtatccttgtgttaatctgtctatagttagtatccattagttatttgactctttctagcttacatttgtaatctacaaatgtttgcttattcagTGGGAATCATTAATAAACATGGGAAAAGACTCGAAGCCAAAGGAGTCAGGAGGGAAGGGAAAGGGGAAACAGGCTGCAAGTGGAAGTGATGAGAATGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
-tgcttgt
- - - - - ccttgtg
- - - - - - - - - - - ctgtcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttaca