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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcatctttttttacaatgaagtgttgtagcagcatgttaggatctaattgcaaggtatgagaattgagttcatcatcatttctctgacaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACA

Basic information

species Glycine max
transcript GLYMA05G30430.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 12
-ttttcatcttttttta-caatgaagtgttgtagcagcatgttaggatctaattgcaaggtatgagaattgagttcatcatcatttctctgacaattg--atagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACA
  |    |   | || | ||  ||||||   |    || | ||    | | || |  |  |||||    |    |  | ||  ||     || | |||  | ||||||| || || || |||||||||||| | ||||| ||||| ||  ||||||| |  |||||||| |||||||||||||| || ||||||||||||||||
cataaagtggctattgagcatcgaagtgcatt----gcttttttcattttgatggttatttatgaattctattatggttattcttgactggaaacttgttacagGTTGTAAAAAGTTTTTCATCTGGTAAACGGGAAGGGGGAGATTTCCTTGCAGCTTCCGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA

upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 12
-ttttcatctttttttacaatgaagtgttgtagcagcatgttagg-atctaattgcaaggtatgagaattgagttcatcatcatttctctgacaattgat---agGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACA
 ||  ||     | |   |   |||    |       || | ||  || ||| ||  |  | |     |||      | || ||| |  ||| ||||  |   ||||||||||||| |||||||| |||||  ||||||| ||||| ||||||||||| |  |||||||| |||||||||||||| || ||||||||||||||||
tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttgg-----ttatgattgccttgaaaatttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA

upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 13
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 13
ttttcatcttttttta-caatgaagtgttgtagcagcatgttaggatctaattgcaaggtatgagaattgagttcatcatcatttctctga--caattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACA
      |   |||  | ||| |   |  || |      ||| |   ||  ||  |||   |  |  ||||    |||  |  | | |  ||  |  ||   ||||||||||||| |||||||| ||||| || ||||| ||||| ||||| ||||| ||||| ||  | |||||||| ||||| |||||  | || |||||||
-----gtaaatttccagcaacggtctcctgcaaatcagtgtcattgtc--atgccaaa--actaagattgttcacatgcttctatattggaatccttttgcagGTTGTGAAGAGTTTCTCATCCGGTAATAGGGAAGGAGGAGATTTTGTAGCAGCATGTGTATCTACAAAAGGAGATTGGATATACTGCATCGGCGAAGACA

upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
ttttcatctttttttacaatgaagtgttgtagcagcatgttaggatctaattgc--aaggtatgagaattgagttcatcatcatttctctgacaattgat--------agGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACA
            |    ||  ||| |      |     |   || | | ||| |  || || || ||     |||  | ||||        | || || |        ||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||
----------ggtgcgtaaccaaggggaactacgatcagaatggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA

upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 13
lower sequence: EFJ30597 (Selaginella moellendorffii), 3'ss of exon 11
ttttcatctttttttacaatgaagtgttgtagcagcatgttaggatctaattgcaaggtatgagaattgagttcatcatcatttctctgacaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACA
                                      ||     |||  || |      |      ||| ||   | |     || ||   ||||  ||||||| ||||||||||| ||||| |||||||| || || || || || || ||||| || || || |||||||| |||||||| || ||||| |||||||
--------------------------------------gtgcatttctcctttc----ctttgtgcctgatttttcccttccggctttgc--attggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA

upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 13
lower sequence: EFJ15973 (Selaginella moellendorffii), 3'ss of exon 11
ttttcatctttttttacaatgaagtgttgtagcagcatgttaggatctaattgcaaggtatgagaattgagttcatcatcatttctctgacaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACA
                                          |    |   | |      |      ||| ||   | |     || ||   ||||  ||||||| ||||||||||| ||||| |||||||| || || || || || || ||||| || || || |||||||| |||||||| || ||||| |||||||
------------------------------------------gtgcatttctccttttctttgtgcctgatttttcccttccggctttgc--attggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA

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|208117434|gb|GD919132.1|GD919132
EST:     TTGTTTGTAACAAAACGTCATCCATATATATCATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCA
genomic: TTGTTTGTAACAAAACGTCATCCATATATATCATGACACTTCAAGGACAGgtatacataa ... caattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCA
EST: gi|193366687|gb|FK332423.1|FK332423
EST:     TATATATCATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCATCTGATAAAAGAGAAGGCGGAGACTTTGTTGCA
genomic: TATATATCATGACACTTCAAGGACAGgtatacataa ... caattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCA
EST: gi|207778029|gb|GD747094.1|GD747094
EST:     TTTTGTTAACTAAAACGTCATCCATATATATCATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCA
genomic: -TTTG-TAAC-AAAACGTCATCCATATATATCATGACACTTCAAGGACAGgtatacataa ... caattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCA
EST: gi|213619985|gb|DB976961.1|DB976961
EST:     TTGTTTGTAACAAAACGTCATCCATATATATCATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCA
genomic: TTGTTTGTAACAAAACGTCATCCATATATATCATGACACTTCAAGGACAGgtatacataa ... caattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCA
EST: gi|193668798|gb|FK609032.1|FK609032
EST:     TTGTTTGTAACAAAACGTCATCCATATATATCATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCATCTGGT
genomic: TTGTTTGTAACAAAACGTCATCCATATATATCATGACACTTCAAGGACAGgtatacataa ... caattgatagGTTGTGAAGAGCTTCTCATCTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaattgcaaggtatgagaattgagttcatcatcatttctctgacaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACA
                                       ctctgac  putative branch site (score: 3)
                                              aattgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcatctttttttacaatgaagtgttgtagcagcatgttaggatctaattgcaaggtatgagaattgagttcatcatcatttctctgacaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - -tgaagtg
- - - - - - - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcaagg