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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagtatttccttttgatattaaatgatattagttatgtatttctgctgtacttccataattaattggtgactgtagtgtatgcttcaatttatcctttgcttatactgaatggtatatattatcagatacaagtttttctaatagaaattcatcaacttcttgcagCTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCAAGAATTGGTAACAAAAATTGGTAAAATATTTGGAGCGATTTTAGAAGAG

Basic information

species Glycine max
transcript GLYMA02G45140.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G45140.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaaaagtatttccttttgatattaaatgatattagttatgtatttctgctgtacttccataattaattggtgactgtagtgtatgcttcaatttatcctttgcttatactgaatggtatatattatcagatacaagtttttctaatagaaattcatcaacttcttgcagCTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCAAGAATTGGTAACAAAAATTGGTAAAATATTTGGAGCGATTTTAGAAGAG
                                                                        |  ||   || ||  ||| ||||     || | |  |     |  |   | || | | |    |    |   | | | ||||| |    |||| | |||||||| || |||||||||||||| || |||||||| ||||||||||||||  | |||||   ||  ||||     ||||| ||||||
------------------------------------------------------------------------gtttgct-tgaatatttcgattt---tgttacctccatctttttattcttgtt-tgacaccttaaaactcacagt-gcaattcttttgtttct-gtagCTATGCTCTGTTTGATATGGATGGCAACCAAGTTCCTCAAGAATTGGTAACTCAGATTGGCGTAACGTTTGAGCGTATTTTGGAAGAG

upper sequence: GLYMA02G45140.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 4
gtaaaagtatttccttttgatattaaatgatattagttatgtatttctgctgtacttccataattaattggtgactgtagtgtat-gcttcaatttatcctttgcttatactgaatggtatatattatcagatacaagtttttctaatagaaattcatcaacttcttgcagCTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCAAGAATTGGTAACAAAAATTGGTAAAATATTTGGAGCGATTTTAGAAGAG
                                                           ||  |    |    | || |    ||    ||||   | ||||   || |  | | |  |  |||||||  | |  | ||  || | || |             |  ||||||||||| || |||||||||||||||||||||||||| |||||||| ||   | | ||||||  |  |||||     ||||| ||||||
-----------------------------------------------------------attgtagcatttccaatgcaaaaaattatctcaaagaaaccttcttttgttatca-tactccatattattggttttaggtgattattattg-----------tcttatgcagCTATGCCCTCTTTGATATGGATGGGAATCAAGTTCCTCAAGAATTAGTCCGAGAGATTGGTGTAGCATTTGAGAAAATTTTGGAAGAG
















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|151411092|gb|EV280903.1|EV280903
EST:     TACCGTACTAGTGAGGATAATTCTGTCCTTTATGACCACGATTTGGAAAG                         CTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCAAGAATTGGTAAC
genomic: TACCGTACTAGTGAGGATAATTCTGTCCTTTATGACCACGATTTGGAAAGgtaaaagtat ... cttcttgcagCTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCAAGAATTGGTAAC
EST: gi|254324811|gb|GR834236.1|GR834236
EST:     TACCGTACTAGTGAGGATAATTCTGTCCTTTATGACCACGATTTGGAAAG                         CTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCA
genomic: TACCGTACTAGTGAGGATAATTCTGTCCTTTATGACCACGATTTGGAAAGgtaaaagtat ... cttcttgcagCTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCA
EST: gi|15814789|gb|BI787064.1|BI787064
EST:     TACCGTACTAGTGAGGATAATTCTGTCCTTTATGACCACGATTTGGAAAG                         CTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCAAGAATTGGTAAC
genomic: TACCGTACTAGTGAGGATAATTCTGTCCTTTATGACCACGATTTGGAAAGgtaaaagtat ... cttcttgcagCTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCAAGAATTGGTAAC
EST: gi|23059794|gb|BU578393.1|BU578393
EST:     CCGTACTAGTGAGTGTATAATTCTGTCCTTTATGACCACGATTTGGAAAG                         CTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCAAGAATTGGTAAC
genomic: CCGTACTAGTGAG-G-ATAATTCTGTCCTTTATGACCACGATTTGGAAAGgtaaaagtat ... cttcttgcagCTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCAAGAATTGGTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatatattatcagatacaagtttttctaatagaaattcatcaacttcttgcagCTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCAAGAATTGGTAACAAAAATTGGTAAAATATTTGGAGCGATTTTAGAAGAG
                         ttctaat  putative branch site (score: 2)
                                             cttcttgc  putative PPT
                      tttttctaatagaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagtatttccttttgatattaaatgatattagttatgtatttctgctgtacttccataattaattggtgactgtagtgtatgcttcaatttatcctttgcttatactgaatggtatatattatcagatacaagtttttctaatagaaattcatcaacttcttgcagCTATGCACTTTTTGATATGGATGGGAATCAAGTTCCCCAAGAATTGGTAACAAAAATTGGTAAAATATTTGGAGCGATTTTAGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG