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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgattctgaacaacaatgatatttctttcaagctcaaattttgttgctatctaactcattaatgttaattggtggtggttgactttgtcaaattgcagCAATGATGGGTTGCTAGCTTTTGTGGAGAACTTTGTGAAGGACCACTTTTTACCAACTATGTTTGTAGACTACCGAAAAGGCGTACAGCAAGCCATATCG

Basic information

species Glycine max
transcript GLYMA20G32370.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32370.1 (Glycine max), 3'ss of exon 15
lower sequence: AT3G10380.1 (Arabidopsis thaliana), 3'ss of exon 15
---------------------------------attgattctga-acaacaatgatattt-ctttcaagctcaaatt----ttgttgctatctaactcattaa-----tgttaat-tggtggtggttgactttgtca-aattg---cagCAATGATGGGTTGCTAGCTTTTGTGGAGAACTTTGTGAAGGACCACTTTTTACCAACTATGTTTGTAGACTACCGAAAAGGCGTACAGCAAGCCATATCG
                                   | || |||  | | |||   || || ||  ||||| |||| |    || ||| | ||| |     | |     || || | |  |     | |  ||  | | |||||   ||| |||||||| |||||  | ||    || |||||||||||||||||  | ||||| || |||||||| |||||  | ||||||||||||||||| ||||| 
gtaagttcaaaatttccacttttctttgaaggctgtcatcctggcaaagcaaaactacttgctcacaagcccaaaatgaaattattgttttctcaagtgctgagaaattgctagtatattcaccatcgggttattaataattgatgcagGAATGATGGATTGCTTACATTCACTGAAAACTTTGTGAAGGACCATCTGTTACCGACAATGTTTGTGGACTATAGGAAAGGCGTACAGCAAGCTATATCA

upper sequence: GLYMA20G32370.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv13s0019g04770.t01 (Vitis vinifera), 3'ss of exon 13
---attgattctg-aacaacaatgatatttctttcaagctcaaattttgttgctatctaactcattaatgttaattggtggtggttgactttgtcaaattgcagCAATGATGGGTTGCTAGCTTTTGTGGAGAACTTTGTGAAGGACCACTTTTTACCAACTATGTTTGTAGACTACCGAAAAGGCGTACAGCAAGCCATATCG
    |  ||| |   | |   ||| |     || |    || ||| | |    | |||  |  |||||||  | |  ||  |   ||   |  | || ||| || |||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||| ||||| 
gaagtgaattttatgaaagggatgttgccaattcctctttccaatgt-gccatt-tcttccatattaatgcgattctgtatta--tggactactgaatttgtagGAATGATGGCTTGCTAGCTTTTGTGGAGAACTTTGTGAAGGACCACTTTTTACCAACGATGTTTGTAGATTACCGAAAAGGCGTACAGCAAGCTATATCA
















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|18735360|gb|BM528721.1|BM528721
EST:     TTCACAGATAAAGTTGCTTCAATGCTGCCAACAAAGTATTCCCAACTCGG                         CAATGATGGGTTGCTAGCTTTTGTGGAGAACTTTGTGAAGGACCACTTTTT
genomic: TTCACAGATAAAGTTGCTTCAATGCTGCCAACAAAGTATTCCCAACTCGGgtgagctcag ... caaattgcagCAATGATGGGTTGCTAGCTTTTGTGGAGAACTTTGTGAAGGACCACTTTTT
EST: gi|207693850|gb|GD675621.1|GD675621
EST:     TGCTGCCAACAAAGTATTCCCAACTCGG                         CAATGATGGGTTGCTAGCTTTTGTGGAGAACTTTGTGAAGGACCACTTTTT
genomic: TGCTGCCAACAAAGTATTCCCAACTCGGgtgagctcag ... caaattgcagCAATGATGGGTTGCTAGCTTTTGTGGAGAACTTTGTGAAGGACCACTTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctatctaactcattaatgttaattggtggtggttgactttgtcaaattgcagCAATGATGGGTTGCTAGCTTTTGTGGAGAACTTTGTGAAGGACCACTTTTTACCAACTATGTTTGTAGACTACCGAAAAGGCGTACAGCAAGCCATATCG
                                       ctttgtc  CT-rich tract
            tcattaatgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgattctgaacaacaatgatatttctttcaagctcaaattttgttgctatctaactcattaatgttaattggtggtggttgactttgtcaaattgcagCAATGATGGGTTGCTAGCTTTTGTGGAGAACTTTGTGAAGGACCACTTTTTACCAACTATGTTTGTAGACTACCGAAAAGGCGTACAGCAAGCCATATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- -gattctg
- - - - - aacaaca
- - - - - - - - - - - - - - ttcaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gactttg