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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacatgttaattgtcaatttttttcattgaagtaatgcattttttgtgttcactttttaaaaaaatgagtttttatgatgtgaatgcattaatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTATCATGAAATGGGGACCAAAGGAGGGCAGACAAGGAAGGAACAGATGGGG

Basic information

species Glycine max
transcript GLYMA18G43320.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G43320.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0105g00600.t01 (Vitis vinifera), 3'ss of exon 1
---cacatgttaattgtcaattttttt-cattgaagtaatgcattttttgtgttcactttttaaaaaaatgagtttttatgatgtgaatgcattaatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTATCATGAAATGGGGACCAAAGGAGGGCAGACAAGGAAGGAACAGATGGGG------
    | |  ||  |  | || | |       ||||||  ||||||  || || |      ||||  |  || |||| ||     || || |||| |||   |||| | |||   |||||||||||||||||| ||||||| ||  ||||||||||  | ||  |||| | ||||||||| ||||| |||||||| ||| |||||      
gcataaacattcgtaataaactatgcaatggtgaagt--tgcattgcttatgata-----ttaaggagttgggtttgtac----tgtattcattgatg--aaggacgaagCAAAGGAGGGCAGACGAGGAAGGAGCAGCTGGGAACAGAGGGGTACAAGGAGCTGGGAAGCAAAGGAGGACAGACGAGGAAGGAGCAGTTGGGGACAGAG
















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|298191050|gb|HO038529.1|HO038529
EST:     GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGG                         AAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
genomic: GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGGcatgcaatac ... aatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
EST: gi|298191202|gb|HO038681.1|HO038681
EST:     GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGG                         AAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
genomic: GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGGcatgcaatac ... aatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
EST: gi|7146042|gb|AW507964.1|AW507964
EST:     GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGG                         AAGGAGCCGTGGAGGGCAGACGATGAAGCATCAGCTAGGGTCAGAGGGGTA
genomic: GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGGcatgcaatac ... aatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
EST: gi|298189522|gb|HO037925.1|HO037925
EST:     GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGG                         AAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
genomic: GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGGcatgcaatac ... aatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
EST: gi|298183271|gb|HO028484.1|HO028484
EST:     GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGG                         AAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
genomic: GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGGcatgcaatac ... aatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
EST: gi|298177761|gb|HO027314.1|HO027314
EST:     GGAGGAACTGGTGGGAAGAGTCTTGATGCTCAAGAACATCTTGCTGAGGG                         AAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTATGGTCAGAGGGGTA
genomic: GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGGcatgcaatac ... aatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
EST: gi|298181075|gb|HO022514.1|HO022514
EST:     GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGG                         AAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
genomic: GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGGcatgcaatac ... aatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
EST: gi|192296499|gb|FG989115.1|FG989115
EST:     GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGG                         AGGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
genomic: GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGGcatgcaatac ... aatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
EST: gi|298181325|gb|HO022764.1|HO022764
EST:     GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGG                         AAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
genomic: GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGGcatgcaatac ... aatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
EST: gi|298168425|gb|HO009355.1|HO009355
EST:     GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGG                         AAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
genomic: GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGGcatgcaatac ... aatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
EST: gi|298198684|gb|HO042047.1|HO042047
EST:     GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGG                         AAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA
genomic: GGAGGAACTGGTGGGAAGAGTCTTGAGGCTCAAGAACATCTTGCTGAAGGcatgcaatac ... aatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttcactttttaaaaaaatgagtttttatgatgtgaatgcattaatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTATCATGAAATGGGGACCAAAGGAGGGCAGACAAGGAAGGAACAGATGGGG
                                         cattaat  putative branch site (score: 3)
      actttttaaaaaaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacatgttaattgtcaatttttttcattgaagtaatgcattttttgtgttcactttttaaaaaaatgagtttttatgatgtgaatgcattaatgtgtaggAAGGAGCCGTGGAGGGCAGACGAGGAAGCAGCAGCTAGGGTCAGAGGGGTATCATGAAATGGGGACCAAAGGAGGGCAGACAAGGAAGGAACAGATGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
cacatgt
- - - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgca