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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtttcttgttatgtagatttgtatattcatagaaattgacttgcttggttgaattaaatctaatgctctgtcatttattactgttgtaatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACGCAGAGCTTTCTGACATGGGAAAGTTTAG

Basic information

species Glycine max
transcript GLYMA10G06590.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 3
ttttgtttcttgttatgtagatttgtatattcatagaaattgacttgcttggttgaattaaatctaatgctctgtcatttattactgttgtaatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACGCAGAGCTTTCTGACATGGGAAAGTTTAG
    ||  |  ||    |    |  |   |||  |  |  |  || | |    || ||| | | ||      | | |  | || || |||   |  | || ||||| | |  || |  || ||||||||||||||||| |||||||| || || ||| |||| || |||||  |||| |||||||| |||||||| || |
----gtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgt-ttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG

upper sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g16900.1 (Oryza sativa), 3'ss of exon 2
-ttttgtttcttgttatgtagatttgtatattcatagaaattgacttgcttggttgaattaaatctaatgctctgtcatttattactgttgtaatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACGCAGAGCTTTCTGACATGGGAAAGTTTAG
   | ||  |  ||    |    |  |   |||  |  |  |  || | |    || ||| | | ||      | | |  | || || |||   |  | || ||||| | |  || |  || ||||||||||||||||| |||||||| || || ||| |||| || |||||  |||| |||||||| |||||||| || |
aaatggtgccaagtgccttctgatcatgctttctgactatgtagctcgttcttatgtatttattatatcttagtttgaacttttccttttgctgt-ttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG

upper sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 1
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------ttttgtttcttgttatgtagatttgtatattc-atagaaattgacttgcttggttgaattaaatctaatgctctgtcatttattactg----ttgtaat-acttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACGCAGAGCTTTCTGACATGGGAAAGTTTAG
                                       || ||    |  |  |   ||  |   | ||  || ||| ||     | |   |||    || ||      | |||   |  ||  ||    ||||| | |   || | ||   | |||||| ||| ||||| || |||||||| |||||||| || ||||| || || || ||||| ||||| ||  |||||||||||||| | |
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggcaattttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG

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|15664371|gb|BI701742.1|BI701742
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|192302073|gb|FG993457.1|FG993457
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|254329852|gb|GR839405.1|GR839405
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|298195797|gb|HO044188.1|HO044188
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|14259098|gb|BG882006.1|BG882006
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|151393897|gb|EV263768.1|EV263768
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|19268871|gb|BM885127.1|BM885127
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|7796143|gb|AW781540.1|AW781540
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTTCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|213602099|gb|DB962592.1|DB962592
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|298166544|gb|HO009983.1|HO009983
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|209725272|gb|BW672747.1|BW672747
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|192328451|gb|FK020725.1|FK020725
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|209700402|gb|BW664415.1|BW664415
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|7478024|gb|AW666107.1|AW666107
EST:     CTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: CTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|8286498|gb|BE024057.1|BE024057
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|298171951|gb|HO021543.1|HO021543
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|209702969|gb|BW656039.1|BW656039
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|8285773|gb|BE023332.1|BE023332
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
EST: gi|37996619|gb|CF808208.1|CF808208
EST:     TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAG                         ATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA
genomic: TCTTCCCCGGCGACGGCATCGGCCCCGAGATCGCCGATTCCGTCAAACAGgtcccttcct ... taatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttggttgaattaaatctaatgctctgtcatttattactgttgtaatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACGCAGAGCTTTCTGACATGGGAAAGTTTAG
                atctaat  putative branch site (score: 3)
       ttgaattaaatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtttcttgttatgtagatttgtatattcatagaaattgacttgcttggttgaattaaatctaatgctctgtcatttattactgttgtaatacttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACGCAGAGCTTTCTGACATGGGAAAGTTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT