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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtggaaaaaaaaattacacaagtgtatatacttaaattgattctttgtgatcaagctaataatactggttttttttctctctttttttgttgcttgaagTTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGATAAAATTGCTATTTGGACTA

Basic information

species Glycine max
transcript GLYMA13G29420.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G29420.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G18040.1 (Arabidopsis thaliana), 3'ss of exon 2
tgtggaaaaaaaaattacacaagtgtatatactta-aattgattctttgtgatcaagct-aataatactggttttttttctctctttttttgttgcttgaagTTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGATAAAATTGCTATTTGGACTA
 ||         | ||   |   | | |  |||   || |  | | |  | ||| |  | |||   || ||||||| || |  | |  || |||      ||||| | ||  |||||||||| ||||||||||| |||||||||||||||||||| ||||| ||  | ||| | | ||| || |  ||  ||||||||||||
-gtacggtttcta-ttcttcttttattttgactcgtaactcctgcgtcatcatccaattgaatctcaccggtttttctttttacatgcttggttt-----agTTGCTTGCATTGATTGGAGAGCAGTTTGATCATGGAGATGAAATATGTGGAGCAGTTGTCAACATTAGAGGAAAGCAAGAAAGGATATCTATTTGGACTA

upper sequence: GLYMA13G29420.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0003g02250.t01 (Vitis vinifera), 3'ss of exon 2
tgtggaaaaaaaaattacacaagtgtatatacttaaattgattctttgtgatcaagctaataatactggttttttttctctctttttttgttgcttgaagTTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGATAAAATTGCTATTTGGACTA
               ||  |    |  | |||  |||||   | ||     | ||  |  ||||  ||| || |  ||| ||  | | || | ||   ||||| | || ||||| ||||||||||||||||| ||||||||||| |||||||| ||  | |||||||||  ||| ||||| ||||| ||| | ||||| |
--------------gtatgctttaggctgtacagaaattttatgttgagccttaaatttttaatg-tggcttctaatct-tcaatatatgctact---agTTGCTAGCCATGATCGGAGAACAGTTTGATCATGGAGATGAAATCTGTGGAGCAGTGATCAATGTCAGAGCTAGACAGGAGAAAATAGCTCTATGGACCA
















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|193675022|gb|FK614362.1|FK614362
EST:     GGACTATGACCTTCCCAAGGGGAAAATCTGATACCAGTTGGTTGTATACG                         TTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGA
genomic: GGACTATGACCTTCCCAAGGGGAAAATCTGATACCAGTTGGTTGTATACGgtattgtttt ... ttgcttgaagTTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGA
EST: gi|298181021|gb|HO022460.1|HO022460
EST:     GGACTATGACCTTCCCAAGAGGAAAATCTGATACCAGTTGGTTGTATACG                         TTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGA
genomic: GGACTATGACCTTCCCAAGGGGAAAATCTGATACCAGTTGGTTGTATACGgtattgtttt ... ttgcttgaagTTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGA
EST: gi|207730120|gb|GD708352.1|GD708352
EST:     GGACTATGACCTTCCCAAGGGGAAAATCTGATACCAGTTGGTTGTATACG                         TTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGA
genomic: GGACTATGACCTTCCCAAGGGGAAAATCTGATACCAGTTGGTTGTATACGgtattgtttt ... ttgcttgaagTTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGA
EST: gi|23729050|gb|BU762604.1|BU762604
EST:     GGACTATGACCTTCCCAAGGGGAAAATCTGATACCAGTTGGTTGTATACG                         TTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGA
genomic: GGACTATGACCTTCCCAAGGGGAAAATCTGATACCAGTTGGTTGTATACGgtattgtttt ... ttgcttgaagTTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGA
EST: gi|254329725|gb|GR839278.1|GR839278
EST:     GGACTATGACCTTCCCAAGGGGAAAATCTGATACCAGTTGGTTGTATACG                         TTGT-GGCGATGAT
genomic: GGACTATGACCTTCCCAAGGGGAAAATCTGATACCAGTTGGTTGTATACGgtattgtttt ... ttgcttgaagTTGTTGGCGATGAT
EST: gi|9986906|gb|BE661014.1|BE661014
EST:     GGACTATGACCTTCC-AAGGGGAAAATCTGATACCAGTTGGTTGTATACG                         TTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGA
genomic: GGACTATGACCTTCCCAAGGGGAAAATCTGATACCAGTTGGTTGTATACGgtattgtttt ... ttgcttgaagTTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgatcaagctaataatactggttttttttctctctttttttgttgcttgaagTTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGATAAAATTGCTATTTGGACTA
         agctaat  putative branch site (score: 3)
                    ctggttttttttctct  putative PPT
            taataatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtggaaaaaaaaattacacaagtgtatatacttaaattgattctttgtgatcaagctaataatactggttttttttctctctttttttgttgcttgaagTTGTTGGCGATGATTGGAGAACAGTTTGATCACGGAGATGAAATATGTGGAGCTGTTGTGAATGTCAGAAGTAGGCAGGATAAAATTGCTATTTGGACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - -aaaaaaa
- - - - - - - - - -caagtgt
- - - - - - - - - - - - - - - - - - - - - -ctttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - caagcta