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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttaagtaacttataattgtgactttctatgtatggatctttccgcaattctgaatgttatttttccattaagttaatctaaaagtcatcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGTGGAGGTGGTGCATCTGCCCTTGTTGTTGAGCTTCTGTAAAACCTATTTT

Basic information

species Glycine max
transcript GLYMA02G47860.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 13
--attttaagtaacttataattgtgactttctatgt-atggatctttccgcaattctgaatgttatttttccattaagttaatctaaaagtcatcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGTGGAGGTGGTGCATCTGCCCTTGTTGTTGAGCTTCTGTAAAACCTATTTT
  ||||    ||        || |    || ||| | || |||      | |  |||   | | ||||| |  | |   | ||   | | |  |    |||||||||||| ||||||  ||||||| || ||||| |||||  ||||||| ||||||||||||||||| || || ||||| |||||| |||||  | | || |
gtatttgtgctataaccctgttattttattttattttattgatagaggagaacctcttcttat-attttactctcatactcatactacaatggt--gttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGTGGAGGTGGTGCATCAGCACTAGTTGTAGAGCTTGTGTAAGCCTTGTTAT
















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|207774060|gb|GD745548.1|GD745548
EST:     GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG                         GTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
genomic: GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctc ... tcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
EST: gi|208064240|gb|GD866622.1|GD866622
EST:     GCATTCTGGTGACACTTTTGGGG                         GTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
genomic: GCATTCTGGTGACACTTTTGGGGgtatgtgctc ... tcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
EST: gi|209708681|gb|BW678862.1|BW678862
EST:     GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG                         GTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
genomic: GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctc ... tcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
EST: gi|193353615|gb|FK319383.1|FK319383
EST:     GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG                         GTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
genomic: GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctc ... tcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
EST: gi|193655659|gb|FK601429.1|FK601429
EST:     GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG                         GTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
genomic: GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctc ... tcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
EST: gi|193383945|gb|FK351350.1|FK351350
EST:     GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG                         GTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
genomic: GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctc ... tcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
EST: gi|208328556|gb|GE129700.1|GE129700
EST:     TCATCCTCTTGGTTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG                         GTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
genomic: TCATCCTCTTGG-TTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctc ... tcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
EST: gi|5761368|gb|AI966727.1|AI966727
EST:     GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG                         GTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
genomic: GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctc ... tcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
EST: gi|193329280|gb|FK296518.1|FK296518
EST:     GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG                         GTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
genomic: GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctc ... tcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
EST: gi|209700567|gb|BW670311.1|BW670311
EST:     GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG                         GTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
genomic: GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctc ... tcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
EST: gi|193483091|gb|FK448428.1|FK448428
EST:     GCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG                         GTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
genomic: GCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctc ... tcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
EST: gi|10253461|gb|BE821227.1|BE821227
EST:     GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGG                         GTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT
genomic: GTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctc ... tcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcaattctgaatgttatttttccattaagttaatctaaaagtcatcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGTGGAGGTGGTGCATCTGCCCTTGTTGTTGAGCTTCTGTAAAACCTATTTT
                                 atctaaa  putative branch site (score: 3)
              ttatttttccattaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttaagtaacttataattgtgactttctatgtatggatctttccgcaattctgaatgttatttttccattaagttaatctaaaagtcatcacctgcagGTACTGAAGCAGAAGAATGGGAAGTACGGAGTTGGTGGCATTTGCAACGGTGGAGGTGGTGCATCTGCCCTTGTTGTTGAGCTTCTGTAAAACCTATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - gtgactt
- - - - - - - - - - - - - - - -tgtatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - ctgaatg