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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACGCCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaactaacttaaatatttattcattctcttctatttcaatgcattcctgagacatttttgttaccaaaatcttatcacag

Basic information

species Glycine max
transcript GLYMA03G21690.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G21690.1 (Glycine max), 5'ss of exon 9
lower sequence: AT5G48570.1 (Arabidopsis thaliana), 5'ss of exon 9
CACGCCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaactaacttaaatatttattcattct-cttctatttcaatgcattcctgagacatttttgttaccaaaatcttatcacag
||| |  || | ||| |||||||| || ||||||||||||||||| ||||  || || |||||||| ||||| ||||||||||| || |||||||||| |||  |   |  |      | |||||  | |     ||| | |||       ||  | |||   ||||   | |||  | | ||  |||
CACACAGGAAAGGATAGAAGCTGCAGGCAAGAAGAAAGAAGAAGGCAATGTGTTGTTCAAAGCTGGAAAATACGCAAGAGCTTCAAAGAGATACGAGAGGgtt-tgggatttggtcctagtatttgctaaagaaacttatgttt-------ttgtttaga---ttttaacatcaagttttgattgcag

upper sequence: GLYMA03G21690.1 (Glycine max), 5'ss of exon 9
lower sequence: AT3G25230.1 (Arabidopsis thaliana), 5'ss of exon 9
CACGCCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaactaacttaaatatttattcattctcttctatttcaatgcattcctgagacatttttgttaccaaaatcttatcacag
|||    |||||||||||||||||| |||||||||| |||||||||||| |    |||||||  || |||||| |    ||||| || ||||| |||||||||    | || ||||         | | |||   || |   | |    | ||     |||| ||   |    || | |  || |||
CACTGAGGAGAAGATTGAAGCTGCTAGTAAGAAGAAGGAAGAAGGAAATTCCAAGTTTAAAGGAGGCAAATATTCCCTGGCTTCCAAGAGATATGAGAAGgtatatgatacgaact---------acttattgctttatgagttat--aagtcgaacaacatcttacatggttaagtttcttctcag

upper sequence: GLYMA03G21690.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv00s0958g00020.t01 (Vitis vinifera), 5'ss of exon 5
CACGCCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaactaacttaaatatttattcattctcttctatttcaatgc-attcctgagacatttttgttaccaaaatcttatcacag-----
|||   |||||||||||| |||||||| |||||||| |||||||| ||||   |||| || |||||||||||||||||||| || || ||||| |||||||||| |  |  |     | ||  ||| ||  |   ||     ||  ||| ||||||  | | |   | |  |     | |  |  ||      
CACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAAGAGCCTCAAAGAGATATGAGAAGgtaaaatcatatgtggaatatgcttagtctattgattagcggtctctgccattcctctgtcctcaatttatctttcttttggttgcaatgcag

upper sequence: GLYMA03G21690.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv00s0769g00010.t01 (Vitis vinifera), 5'ss of exon 9
CACGCCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaactaacttaaatatttattcattctcttctatttcaatgc-attcctgagacatttttgttaccaaaatcttatcacag-----
|||   |||||||||||| |||||||| |||||||| |||||||| ||||   |||| || |||||||||||||||||||| || || ||||| |||||||||| |  |  |     | ||  ||| ||  |   ||     ||  ||| ||||||  | | |   | |  |     | |  |  ||      
CACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAAGAGCCTCAAAGAGATATGAGAAGgtaaaatcatatgtgggatatgcttaatctattgattagcggtctctgccattcctctgtcctcaatttatctttcttttggttgcaatgcag

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|57574028|gb|CX547003.1|CX547003
EST:     CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaa ... cttatcacagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
EST: gi|58014983|gb|CX701725.1|CX701725
EST:     CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaa ... cttatcacagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
EST: gi|192333549|gb|FK026850.1|FK026850
EST:     CATTATTTAAAGCTGGTAAATATGCAAGAGCCTCTAAAAGATACGAGAAG                         ACTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGGAG
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaa ... cttatcacagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
EST: gi|193483590|gb|FK450635.1|FK450635
EST:     CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaa ... cttatcacagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
EST: gi|192316141|gb|FK011584.1|FK011584
EST:     CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaa ... cttatcacagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
EST: gi|192319168|gb|FK009108.1|FK009108
EST:     AAAGATACGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
genomic: AAAGATACGAGAAGgtaataaaaa ... cttatcacagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
EST: gi|6666583|gb|AW278042.1|AW278042
EST:     CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaa ... cttatcacagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
EST: gi|57574341|gb|CX547316.1|CX547316
EST:     CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaa ... cttatcacagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
EST: gi|192316140|gb|FK011583.1|FK011583
EST:     TTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
genomic: TTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaa ... cttatcacagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
EST: gi|10254863|gb|BE822629.1|BE822629
EST:     CATTATTTAAAGNNGGTAAATATGCAAGAGCNTCTAAAAGATACGAGAAG                         GCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG
genomic: CATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaa ... cttatcacagGCTGTAAAGTTCATAGAGTACGATACTGCCTTTAGCGAAGAGGAGAAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACGCCAGAGAAGATTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGCATTATTTAAAGCTGGTAAATATGCAAGAGCTTCTAAAAGATACGAGAAGgtaataaaaactaacttaaatatttattcattctcttctatttcaatgcattcctgagacatttttgttaccaaaatcttatcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT