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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttgactgtggcctgtgtgtatttttatttccttagcttgttcttactaacatatatttgttgaattcaaatagattttgatttttttcctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG

Basic information

species Glycine max
transcript GLYMA01G41100.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 1
tctttgactgtggcctgtgtgtatttttatt-tccttagcttgttct-tactaacatatatttgttgaattcaaatagattttgatttttttcctc----atgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG
          |    || ||  |||| | |  |  || ||||||| |  | |||      || ||  | ||||  |    |   | || ||| |||    |||||||||||||||||||||||||| || ||||| || ||||| ||||||||| |||||||  |||| ||  | ||
-----agtattattttgagttaatttatgtaatttttggcttgttgtacagtaatgctggttagtcta-ttcaggtttgctcaaagttgttttctctggtatgcagGCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG

upper sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
tctttgactgtggcctgtgtgtatttttatttccttagcttgttcttactaacatatatttgttgaattcaaatagattttgatttttttcctc----atgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG
    |   |   |  | | | ||  | |||||  || |||| | | |||   |   |  || ||  |||||  |    |   | || ||| |||    ||||||||||| |||||||||||||| || ||||| || ||||| ||||||||| |||||||  |||| ||  | ||
--cgtaggtcaagtttttttatacctgtatttt-ttggcttat-catacagtctgctggttattctattcaggtttgctcaaagttgttttctctcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG

upper sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
tctttgactgtggcctgtgtgt-atttttatttccttagcttgttcttactaacatatatttgttgaattcaaatagattttgatttttttcctcatg--cagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG
  ||   ||        | ||| |    |  || |||| | |  | ||||  | || |  ||  |   |  || ||| ||||   || |||| | ||   ||||| |||||||||||||||||||||||||| || ||||| |||||||||||||| ||  |||| ||||||||
-tttaagctcctaataatatgtgaaccatgcttgcttatcgtcattttacaga-atgttcttccttt-tctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG

upper sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 1
tctttgactgtggcctgtgtgtatttttatttccttagcttgttcttac---taacatatatttgttgaattcaaat-------agattttgatttttttcctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG
               | |  |||  | |||   | |||||| |||||     |||  |   ||||||  |||    |       || || || | ||  |   ||| |||||||| |||||||| |||||||||||||| || ||||| ||||||||||| || || ||  ||||  | ||
----------ctaaatataggtagctgtatacacctagcttattcttctccataaggtgcttttgttttattttctttttcctaagcttgtgttattaattgacatccagGCTACTATTGGTATCGATTTTCTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTG

upper sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S39_147V6.2 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------tctttgactgtggcctgtgtgtatttttatttccttagcttgttct--tactaacatatatttgttgaattcaaatagatttt------gatttttttcctcat-------gcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG
                                                                       ||  | |||     || ||  |  ||| |||   || | || ||||  ||  ||| | |  | |  |  |  |  | | |  |      || ||||  | | ||       |||||| || ||||||||||||||||| || || || ||||||||||| ||||| |||||| |||| ||| | ||
gttagcttctttccctcctagtcttcttgcataaaaattgtgtgctgctgacatttctggtttgccgtacatcaataactccatactctggatggtttcattctttttgttttttctagtaagaacctgtcctggcaggttcaaggttggtgctattgatgagttttcccttgataactttggcagGCAACTATTGGTATTGATTTTCTCTCCAAGACCATGTATCTTGAGGATCGCACTGTTAGACTACAGCTCTG

upper sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 2
---tctttgactgtggcctgtgtgtatttttat-ttccttagcttgttcttactaacatatatttgttgaattcaaatagattttgatttttttcctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG
   || |   |      |||  || |     || ||  | |  || |    |||   |  | ||   ||  |      | |     ||||| |      ||||||| || ||||| ||||||||||| |||||||| ||||| |||||||| || || || || || ||| | ||
tgttcatgtgcgaaaatctg-atgcacgaaaatattgttcaatttttcaaaacttcgaagtgttctgtggttatggtgataaccaaattttatgtt---tgcagGCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG

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|254315767|gb|GR825576.1|GR825576
EST:     GCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAG                         GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
genomic: GCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccct ... cctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
EST: gi|254337567|gb|GR845244.1|GR845244
EST:     GCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAG                         GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
genomic: GCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccct ... cctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
EST: gi|207803954|gb|GD774019.1|GD774019
EST:     CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAG                         GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccct ... cctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
EST: gi|208286428|gb|GE086514.1|GE086514
EST:     CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAG                         GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccct ... cctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
EST: gi|193541374|gb|FK499126.1|FK499126
EST:     CGATAACTACCTTATTCAG                         GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCG
genomic: CGATAAC-ACC-TA-TCAGgtttgtccct ... cctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCG
EST: gi|254322229|gb|GR837643.1|GR837643
EST:     CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAG                         GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccct ... cctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
EST: gi|254348134|gb|GR851813.1|GR851813
EST:     CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAG                         GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccct ... cctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
EST: gi|192322517|gb|FK014638.1|FK014638
EST:     CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAG                         GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccct ... cctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
EST: gi|208296568|gb|GE089696.1|GE089696
EST:     CCAGCATCATCACTCGCTTCATGTACGATAAATTCGATAACACCTATCAG                         GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTCGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccct ... cctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
EST: gi|254319917|gb|GR830941.1|GR830941
EST:     CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAG                         GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccct ... cctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
EST: gi|193617486|gb|FK568852.1|FK568852
EST:     CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAG                         GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccct ... cctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA
EST: gi|193381439|gb|FK347492.1|FK347492
EST:     CCAGCATCATCACTCGCTTCATGTACGATAAATTCGATAACACCTATCAG                         GCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTCGAAGATCGA
genomic: CCAGCATCATCACTCGCTTCATGTATGATAAATTCGATAACACCTATCAGgtttgtccct ... cctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactaacatatatttgttgaattcaaatagattttgatttttttcctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG
                                ttttgatttttttcct  CT-rich tract
        atatatttgttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttgactgtggcctgtgtgtatttttatttccttagcttgttcttactaacatatatttgttgaattcaaatagattttgatttttttcctcatgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - actgtgg
- - - - - - -cctgtgt
- - - - - - - - - - - - - - - - - - -gcttgtt
- - - - - - - - - - - - - - - - - - - - - - - -actaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaattc