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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaaaaccacagtagataggctctcattttacacatctcactttagggtagtcaaatccttttcattgtagctttgtcctccttaacttggaggtgcagATATTTTTCGACCTTTTGTTGGCTACAAAGAAGTCAGACTTGTTAGCAAGGAATCGAGACAA

Basic information

species Glycine max
transcript GLYMA04G41150.3
intron # 3
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G41150.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0098g01370.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------------------------------tttaaaaccacagtagataggctctcattttacac-------atctcactttagggtagtcaaatccttttcattgtagctttgtcctccttaacttggaggtgcagATATTTTTCGACCTTTTGTTGGCTACAAAGAAGTCAGACTTGTTAGCAAGGAATCGAGACAA
                                                                               ||| || ||    |  | |||  | ||| | | |        |||  | |      | |   ||  |||    | ||  |||||  || | | ||||||  || |||||| ||||| |||||||| |||||||||||||| |||||||| ||||||||||| ||||| 
gtatcctttttttgatccactattttttttgcctagtatgactttcctttttcctcctctattttacaataaaatgccattagaagcagcagaattgggcatttattatgctccactactgtcttgcctagcatcactttcattttttctcctcta-ttttgttttcttca-cttggatttgtagATATCTTTCGCCCTTTTGTAGGCTACAAAGAAGTGAGACTTGTGAGCAAGGAATCAAGACAT
















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|192295845|gb|FG990883.1|FG990883
EST:     ACTGTTTGTGGAGGGCTTGCCTCCCAACTGTACAAGACGGGAAGTAGCTC                         ATATTTTTCGACCTTTTGTTGGCTACAA
genomic: ACTGTTTGTGGAGGGCTTGCCTCCCAACTGTACAAGACGGGAAGTAGCTCgtatcctttc ... ggaggtgcagATATTTTTCGACCTTTTGTTGGCTACAA
EST: gi|58018860|gb|CX705602.1|CX705602
EST:     ACTGTTTGTGGAGGGCTTGCCTCCCAACTGTACAAGACGGGAAGTAGCTC                         ATATTTTTCGACCTTTTGTTGGCTACAAAGAAGTCAGACTTGTTAGCAAGG
genomic: ACTGTTTGTGGAGGGCTTGCCTCCCAACTGTACAAGACGGGAAGTAGCTCgtatcctttc ... ggaggtgcagATATTTTTCGACCTTTTGTTGGCTACAAAGAAGTCAGACTTGTTAGCAAGG
EST: gi|209716114|gb|BW668653.1|BW668653
EST:     ACTGTTTGTGGAGGGCTTGCCTCCCAACTGTACAAGACGGGAAGTAGCTC                         ATATTTTTCGACCTTTTGTTGGCTACAAAAGA-GTCAGACTTGTTAGCAAG
genomic: ACTGTTTGTGGAGGGCTTGCCTCCCAACTGTACAAGACGGGAAGTAGCTCgtatcctttc ... ggaggtgcagATATTTTTCGACCTTTTGTTGGCTACAAA-GAAGTCAGACTTGTTAGCAAG
EST: gi|209697736|gb|BW655639.1|BW655639
EST:     ACTGTTTGTGGAGGGCTTGCCTCCCAACTGTACAAGACGGGAAGTAGCTC                         ATATTTTTCGACCTTTTGTTGGCTACAAAGAAGTC
genomic: ACTGTTTGTGGAGGGCTTGCCTCCCAACTGTACAAGACGGGAAGTAGCTCgtatcctttc ... ggaggtgcagATATTTTTCGACCTTTTGTTGGCTACAAAGAAGTC
EST: gi|58019080|gb|CX705822.1|CX705822
EST:     ACTGTTTGTGGAGGGCTTGCCTCCCAACTGTACAAGACGGGAAGTAGCTC                         ATATTTTTCGACCTTTTGTTGGCTACAAAGAAGTCAGACTTGTTAGCAAGG
genomic: ACTGTTTGTGGAGGGCTTGCCTCCCAACTGTACAAGACGGGAAGTAGCTCgtatcctttc ... ggaggtgcagATATTTTTCGACCTTTTGTTGGCTACAAAGAAGTCAGACTTGTTAGCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggtagtcaaatccttttcattgtagctttgtcctccttaacttggaggtgcagATATTTTTCGACCTTTTGTTGGCTACAAAGAAGTCAGACTTGTTAGCAAGGAATCGAGACAA
                                  ctccttaac  putative branch site 
               ttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaaaaccacagtagataggctctcattttacacatctcactttagggtagtcaaatccttttcattgtagctttgtcctccttaacttggaggtgcagATATTTTTCGACCTTTTGTTGGCTACAAAGAAGTCAGACTTGTTAGCAAGGAATCGAGACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA