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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattcactgcctttattagcttctctcatttatgtgtaattagagttgtggctgtgcattctataacaaacaaattaaatgttggtcaatggttttgcagCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG

Basic information

species Glycine max
transcript GLYMA11G11960.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g10130.1 (Oryza sativa), 3'ss of exon 4
gattcactgcctttattagcttctctcatttatgtgtaattagagt-tgtggctgtgcattctataacaaacaaattaaatgttggtcaatg-gttttgcagCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG
     |   | || |||||  | | | ||| |    ||  |||  | |||   ||  |    |  |  | |  ||  ||    || | | |  ||| | ||| ||||| || |||||||| || |||||||  ||||||||||| |||||||| || ||||| |||||||||
-ccctatgacattgattagtattt-taattcagaattatctagtctatgtaagtggtcccattcaagtagaagaagcaatacatgtttactctgttatccagATACCAAGAGGCAATTGAAGAAATTACCAGGAGAATGGGTGCAGGAATGGCAAAGTTTATATGCAAGGAG

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 4
lower sequence: AT4G34650.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------gattca---ctgcctttattagcttctctcatttatgtgtaattagagttgtggctgtgcattctataacaaacaaattaaatgttggtcaatggttt-tgca-----gCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG
                   ||||    |||  |||  ||  |  |||   | || | |   | ||  |   |   |   |  ||  |     |  ||   | ||  | | |  | | | ||     | || || || || ||||| || || || |||||||||||||| ||||||||||| || ||||||||||||
gttaatttgctatatacaaattctgttctgttttttataaatgttcttgctcatttattgattgatctactgaatttggtgatactaattttatgttttgttttactaacttatatatacaaaaaagGTATCAAGAGGCTATTGAAGATATAACTAAAAGAATGGGTGCAGGAATGGCCAAGTTCATTTGCAAGGAG

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 4
gattcactgcctttattagcttctc-tcatttatgtgtaattagagttgtggctgtgcattctataacaaacaaattaaatgttggtcaatggttttg---cagCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG
  ||      ||| | ||  | | | || | ||| ||  |  | |    ||  |   |||  | || ||||| | |||  ||||   |||    ||||   ||| || ||||| |||||||| ||||| |||||| ||||||| || |||||||| |||||||||||||| |||
-ttttgagttcttgaatatatacacatcttctatctgataaaaaaaaaatgtatacacatcttcta-caaaccactta--tgttatccaaaaaatttgttgcagTTATCAGGAGGCAATTGAAGACATCACCAAACGAATGGGGGCAGGAATGGCAAAATTTATTTGCAAAGAG

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|14010995|gb|BG725917.1|BG725917
EST:     ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGAAAGAA                         CTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGC
genomic: ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAAgtcagttctt ... ggttttgcagCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGC
EST: gi|208160470|gb|GD958766.1|GD958766
EST:     ATGGACCAGTCTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA                         CTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGC
genomic: ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAAgtcagttctt ... ggttttgcagCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGC
EST: gi|209722769|gb|BW682867.1|BW682867
EST:     ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA                         CTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGC
genomic: ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAAgtcagttctt ... ggttttgcagCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGC
EST: gi|27446333|gb|CA953456.1|CA953456
EST:     ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA                         CTACCAGGAAAGCA-TTGAGGACATTACCAAAAGAATGGGTGCTGGAATGG
genomic: ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAAgtcagttctt ... ggttttgcagCTACCAGGAA-GCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGG
EST: gi|20813646|gb|BQ298124.1|BQ298124
EST:     ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA                         CTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGC
genomic: ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAAgtcagttctt ... ggttttgcagCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGC
EST: gi|209725283|gb|BW672760.1|BW672760
EST:     ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA                         CTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGC
genomic: ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAAgtcagttctt ... ggttttgcagCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGC
EST: gi|213595316|gb|DB968448.1|DB968448
EST:     ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA                         CTACCAGGAAGCAATTGAG
genomic: ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAAgtcagttctt ... ggttttgcagCTACCAGGAAGCAATTGAG
EST: gi|209714966|gb|BW650812.1|BW650812
EST:     ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA                         CTACCAGGAAGCAATTGAGGACATTACCAAA
genomic: ATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAAgtcagttctt ... ggttttgcagCTACCAGGAAGCAATTGAGGACATTACCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtggctgtgcattctataacaaacaaattaaatgttggtcaatggttttgcagCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG
               ctataac  putative branch site (score: 3)
            attctataacaaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattcactgcctttattagcttctctcatttatgtgtaattagagttgtggctgtgcattctataacaaacaaattaaatgttggtcaatggttttgcagCTACCAGGAAGCAATTGAGGACATTACCAAAAGAATGGGTGCTGGAATGGCCAAATTTATTTGCAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG