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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaaaatcctagaatttttgcgttacttcagttaaaatgatttttttttgggatggatgtttccattggttcaatgctgtgtccttaattgaatattagCTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAAGCGAAGGCACCGGAAGTAACAAATCAAAAGGGGATTTCACCAGTAAACT

Basic information

species Glycine max
transcript GLYMA05G34330.1
intron # 33
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34330.1 (Glycine max), 3'ss of exon 33
lower sequence: Vv01s0011g06090.t01 (Vitis vinifera), 3'ss of exon 12
tgtaaaatcctagaatttttgcgttacttcagttaaaatgatttttttttgggatg-gatgtttccattggttcaatgctgtgtccttaat-tgaata--ttagCTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAAGCGAAGGCACCGGAAGTAACAAATCAAAAGGGGATTTCACCAGTAAACT--
   |  ||  ||   |  || |  | | |    |||  |||||| | || |   || ||   |    || |     |||  |||||||||| |  ||   ||||  |||||||||| || ||||| ||||||||||| || |||||||| || ||||| ||||| ||||| ||   | |   || | ||||   |   | |  |  
---accattttaatctgatttctgttcgtagtgtaatctgatttctgttcgtagtgtgacaatcatgttagcatgttgc-atgtccttaatctccattgtttagGATGTATGACCGAGAGTGGGATGATGAGAAGAGGCAGAGAGCTGAACAAAAGCGGAGGCATCGGAAATA--GAGTTTGAAAGAGATTATTCTGTTCATGTCC
















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|58023884|gb|CX710625.1|CX710625
EST:     ATTCACGGTAAAGAGGCGGCCAGCAAGTTGAATCGCCGTGATTCAGATCC                         CTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAA
genomic: ATTCACGGTAAAGAGGCGGCCAGCAAGTTGAATCGCCGTGATTCAGATCCgtatccttaa ... tgaatattagCTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAA
EST: gi|7926511|gb|AW832537.1|AW832537
EST:     ATTCACGGTAAAGAGGCGGCCAGCAAGTTGAATCGCCGTGATTCAGATCC                         CTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAA
genomic: ATTCACGGTAAAGAGGCGGCCAGCAAGTTGAATCGCCGTGATTCAGATCCgtatccttaa ... tgaatattagCTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAA
EST: gi|254345867|gb|GR859514.1|GR859514
EST:     ATTCACGGTAAAGAGGCGGCCAGCAAGTTGAATCGCCGTGATTCAGATCC                         CTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAA
genomic: ATTCACGGTAAAGAGGCGGCCAGCAAGTTGAATCGCCGTGATTCAGATCCgtatccttaa ... tgaatattagCTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAA
EST: gi|209712072|gb|BW674219.1|BW674219
EST:     ATTCACGGTAAAGAGGCGGCCAGCAAGTTGAATCGCCGTGATTCAGATCC                         CTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAA
genomic: ATTCACGGTAAAGAGGCGGCCAGCAAGTTGAATCGCCGTGATTCAGATCCgtatccttaa ... tgaatattagCTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAA
EST: gi|298184868|gb|HO030081.1|HO030081
EST:     ATTCACGGTAAAGAGGCGGCCAGCAAGTTGAATCGCCGTGATTCAGATCC                         CTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGAT
genomic: ATTCACGGTAAAGAGGCGGCCAGCAAGTTGAATCGCCGTGATTCAGATCCgtatccttaa ... tgaatattagCTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGAT
EST: gi|254345866|gb|GR859513.1|GR859513
EST:     ATTCACGGTAAAGAGGCGGCCAGCAAGTTGAATCGCCGTGATTCAGATCC                         CTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAA
genomic: ATTCACGGTAAAGAGGCGGCCAGCAAGTTGAATCGCCGTGATTCAGATCCgtatccttaa ... tgaatattagCTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgggatggatgtttccattggttcaatgctgtgtccttaattgaatattagCTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAAGCGAAGGCACCGGAAGTAACAAATCAAAAGGGGATTTCACCAGTAAACT
                                    gtccttaat  putative branch site 
                                        ttaattgaatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaaaatcctagaatttttgcgttacttcagttaaaatgatttttttttgggatggatgtttccattggttcaatgctgtgtccttaattgaatattagCTTGTATGACCGTGAATGGGAGGATGAGAAGAGACAAAGAGCTGATCAGAAGCGAAGGCACCGGAAGTAACAAATCAAAAGGGGATTTCACCAGTAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - gggatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgct