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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcagttctttcttctgctgctatctgctaaagtattatataatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTGCTGCAATATTCACCAAATCTACGTTGCACCGCT

Basic information

species Glycine max
transcript GLYMA07G08320.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 10
gttagcagttctttcttctgctgctatctgctaaagtattatataatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTGCTGCAATATTCACCAAATCTACGTTGCACCGCT
                   | || |   |    || |       | | || | |   | ||||  |  ||||     | |  |  |    |||||     ||| |||||   ||| | ||||| |||||||| || ||||||||||||||| ||||||| || || |||||| | |||||||| |||
-------------------gttggtggatctctaattccatagcactttagttctacactgatgtaaccttctcacaaaatttttcc---aactg-----cagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT

upper sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 10
----gttagcagttctttcttct-gctgctatctgctaaagtattatataatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTGCTGCAATATTCACCAAATCTACGTTGCACCGCT
    || | || ||||      | | |  ||||||||     |    |    ||| |  |||||| |||  |   |      |  | |   | |    ||  |||||| |||| || ||| ||||||| || ||||| ||||||||||| ||||||||||| || ||||| |||||| |  | |||||||| 
gtttgtcaacaattctaaagggtagatcatatctgctgcccgacatcactg-atatttgataaattatatttctatagccaaaagcttatttaagttttgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAGTATTCGCCAAATTTGAGATGCACCGCC
















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|193510758|gb|FK471246.1|FK471246
EST:     ACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG                         GTTTTTCACAAGAGAATGCCGCCTGAAGCCATGGATCTTGTGTCAAGGCT
genomic: ACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAGgttagcagtt ... tggcttccagGTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCT
EST: gi|207745566|gb|GD715500.1|GD715500
EST:     ACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG                         GTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTG
genomic: ACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAGgttagcagtt ... tggcttccagGTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTG
EST: gi|208189255|gb|GD985633.1|GD985633
EST:     ACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG                         GTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAA
genomic: ACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAGgttagcagtt ... tggcttccagGTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAA
EST: gi|14126698|gb|BG791136.1|BG791136
EST:     ACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG                         GTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTG
genomic: ACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAGgttagcagtt ... tggcttccagGTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTG
EST: gi|8827250|gb|BE210980.1|BE210980
EST:     ACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG                         GTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTG
genomic: ACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAGgttagcagtt ... tggcttccagGTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTGCTGCAATATTCACCAAATCTACGTTGCACCGCT
                               acctgac  putative branch site (score: 3)
                                                cttcc  putative PPT
      ataaatgataaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcagttctttcttctgctgctatctgctaaagtattatataatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTGCTGCAATATTCACCAAATCTACGTTGCACCGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC