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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcagttctttcctctgctgctacctgctaaagtattatatgtaatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT

Basic information

species Glycine max
transcript GLYMA03G01850.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 10
gttagcagttctttcctctgctgctacctgctaaagtattatatgtaatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT
                   | || |   | ||  | |   ||| | | | || | |   | ||||  |  ||||     | |  |  |    |||||     ||| |||||   ||| | ||||||||||||||||| |||||||| |||||| |||| || || || |||||| | |||||||| |||
-------------------gttggtggat-ctctaattccata-gcactttagttctacactgatgtaaccttctcacaaaatttttcc---aactg-----cagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT

upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 10
gttagcagttctttcctctgctgctacctgctaaagtattatatgtaatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT
             |         |||    ||   || || | | | || | | |  |||    |  | |    ||   |    ||| |     || |  |  || |||||   ||| | ||||||||||||||||| ||||| || |||||||| ||||| || |||||||| || || |||||||||
------------gttagggatctctaatctctgtggtgtttttt-tcatttcagctgtaatgagttgacaagctcacctaagtttgatt-----ctcgtgt--agCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT

upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 10
gttagcagttctttcctctgctgctacctgctaaagtattatatgtaatataatccataaatgataaatacttccattcagacctgactgaaaac-tggct-tccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT
                            || ||||  ||   | ||    |  |   |   ||     |  ||| | | | |  | |   |  |  |  || | ||| |||| |||||| |||||||||||||||| || || || || ||||| || ||||| || |||||||| || ||||||||||| 
-------------------------gtttgttaaataatcgcaggtgcc-tctttggtgcgtgt--gcttgttcaaatgaaatttaatgtagcatataactcttcagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA

upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 10
----gttagcagttctttcctct-gctgctacctgctaaagtattatatgtaatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT
    || | || ||||      | | |  || |||||   |    | ||     ||| |  |||||| |||  |   |      |  | |   | |    ||  |||||| |||| || ||| ||||||| || |||||||||||||||||||||||||||||||| ||||| |||||| |  | ||||| || 
gtttgtcaacaattctaaagggtagatcatatctgct---gcccgacatcactgatatttgataaattatatttctatagccaaaagcttatttaagttttgttttccagCTTTTCCATAAGCGAATGCCCCCAGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAGTATTCGCCAAATTTGAGATGCACCGCC

upper sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 9
gttagcagttctttcctctgctgctacctgctaaagtattatatgtaatataatccataaatgataaatacttccattcagac--ctgactgaaaactggcttc-cagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT
                                                         |   |    ||    |   ||  | |    |  |    | |  | |  ||||| ||||||||||||||||| || || |||||||||||||| || || || || ||||| || || ||||| || || | | | 
--------------------------------------------------------gtgcgtaggcaacttctttgttggggcggtcgtttacgtagtaacgtggcagGTGTTTCACAAGAGAATGCCTCCGGAGGCTGTGGATCTTGTCTCGAGACTACTCCAATACTCGCCTAATCTGCGCTGTAGTTCA

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|51335237|gb|CO979103.1|CO979103
EST:     ACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         GTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTG
genomic: ACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAGgttagcagtt ... tggcttccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTG
EST: gi|58020603|gb|CX707345.1|CX707345
EST:     ACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         GTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTG
genomic: ACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAGgttagcagtt ... tggcttccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTG
EST: gi|9898940|gb|BE607908.1|BE607908
EST:     ACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         GTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTG
genomic: ACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAGgttagcagtt ... tggcttccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT
                               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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcagttctttcctctgctgctacctgctaaagtattatatgtaatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT