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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttattttattttatttatttatttcccttttttaatttttaggtttttttttctccttatatgttgtgtgttgatcgttttttctgtatttatca...

Basic information

species Glycine max
transcript GLYMA10G10000.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 3
GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt--ttattttatttatttatttcccttt-tttaatttttaggtttttttttctccttatatgttgtgtgttgatcgttttttctgtatttatca
    | |||  ||||||||| | | | |||||||||   |||||||| |||||||||||||||||||||| |||   |  ||  |     | ||||| |     |  ||   |  ||| | | | |   |  || | |  |   | |  |    ||      || ||    
TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCACAGATGAAGAAGACgtaagtgcctgtttgctgctcctgtttatgtgttggtacttgtgtaatagatctgtgtggatagttgtgtaattgatatgaacaacttaagggctaattt---

upper sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 5'ss of exon 3
GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagt-tattttattttatttatttatttcccttttttaattttta-ggtttttttttctccttatatgt-tgtgtgttgatcgttttttctgtatttatca
||||||||||||||||| || ||| |||| ||||||  |||||| |||||||| ||||||||||| |||||||| || |||| || || |  ||||||    ||| |  | | || | ||||| ||| || ||| ||   | | |    || | | | |   |||  ||  
GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAGGCGCAGATGAAGAAAACgtgagtgtaatttaattcatgttattattttttatttctcttctgtatgatttttctttttcattagataaatattttcaaattgatctata-atatccat--
















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|298196961|gb|HO041704.1|HO041704
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtgaacagTTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|9987770|gb|BE661878.1|BE661878
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtgaacagTTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|15813808|gb|BI786083.1|BI786083
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtgaacagTTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|14205367|gb|BG839045.1|BG839045
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtgaacagTTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|208277056|gb|GE077465.1|GE077465
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtgaacagTTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|151397650|gb|EV267523.1|EV267523
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtgaacagTTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|151408011|gb|EV277826.1|EV277826
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtgaacagTTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|24205496|gb|BU964749.1|BU964749
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACTTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtgaacagTTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|298177257|gb|HO023504.1|HO023504
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCTCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtgaacagTTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|14206051|gb|BG839729.1|BG839729
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttatt ... gtgtgaacagTTTGGCTATGCATGAAGAATCAACGTCTAGGCGCAAGACTGATGATAATGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCACAGATGAAGAAGACgtgagttattttattttatttatttatttcccttttttaatttttaggtttttttttctccttatatgttgtgtgttgatcgttttttctgtatttatca

- - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG