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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGAGCTGCATTCTTATGAGAAGGAAGTTGAGAGAGAAGCTGCCAAAACAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAGgtatatcttctccctctgcatttgctttcaggtgatttgccacatcgggttatgtgttatttacttttctctgttaaaaaaaaattatgcaatttgatggtaaattttgttgagctgatttgcattttgacag

Basic information

species Glycine max
transcript GLYMA13G35770.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G35770.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G30410.1 (Arabidopsis thaliana), 5'ss of exon 2
GAAGGAGCTGCATTCTTATGAGAAGGAAGTTGAGAGAGAAGCTGCCAAAACAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAGgtatatcttctccctctgcatttgctttcaggtgatttgccacatcgggttatgtgtt-atttacttttctctgttaaaaaaaaattatgcaat-ttgatggtaaattttgttgagctgatttgcattttgacag--
||| ||||| || ||||||||||| ||||||||||||||||| || || || |||||||||| ||| ||||| ||||| ||| | || || || ||||||||| |  ||     ||    |||   |    || ||| |     ||||     || ||  ||        |||   ||       || |||  | || |   |   ||||    |     | |   |  |||     
GAAAGAGCTTCACTCTTATGAGAAAGAAGTTGAGAGAGAAGCGGCTAAGACTGCTGATATGAAGGACAAAGGTGCTGATCCCTACGACCTTAAACAACAGgtacagatt-----tcattgtttatctctctgt-attcgaagattcggagcccgtctttgttcgtcagaatctagaaatgctgtgttgtgctgtgtttagacttggtttttcctaatctgtgtatgtggtgatgcag

upper sequence: GLYMA13G35770.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv15s0021g01180.t01 (Vitis vinifera), 5'ss of exon 2
GAAGGAGCTGCATTCTTATGAGAAGGAAGTTGAGAGAGAAGCTGCCAAAACAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAGgtatatcttctccctctgcatttgctttcaggtgat-ttgccacatcgg-gttatgtgttatttacttttctctgttaaaaaaaaattatgcaatttgatggtaaattttgttgagctgatttgcattttgacag
 |||||| | ||||| |||||||| || ||||| ||||||||||| ||||| || ||||||| ||| || |||||||||||  |||| || || ||||||||||  |     ||| | |||||   | ||  |    |    | || || ||||| | |  |    || | | || |      ||| |||  || |  |    |                               
TAAGGAGTTCCATTCCTATGAGAAAGAGGTTGAAAGAGAAGCTGCAAAAACTGCGGATATGAAGGAGAAGGGAGCTGACCCTTATGACCTTAAACAACAGgtatgcccaggtccttttcattt---tccaaatagcatcatgaaattggtgttatatatcttaaggttatgtttggttcctggaaagtat-taagtaaaaaaaa-------------------------------
















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|163922946|gb|EH040178.1|EH040178
EST:     CAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAG                         GAAAATGTGTTGGCAGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAGgtatatcttc ... attttgacagGAAAATGTGTTGGCAGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|16346158|gb|BI971753.1|BI971753
EST:     CAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCTAGCAACAG                         GAAAATGTGTTGGCAGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAGgtatatcttc ... attttgacagGAAAATGTGTTGGCAGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|192324305|gb|FK018281.1|FK018281
EST:     CAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAG                         GAAAATGTGTTGGCAGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAGgtatatcttc ... attttgacagGAAAATGTGTTGGCAGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|192330897|gb|FK023084.1|FK023084
EST:     CAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAG                         GAAAATGTGTTGGCAGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAGgtatatcttc ... attttgacagGAAAATGTGTTGGCAGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|29495571|gb|CB556170.1|CB556170
EST:     CAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAG                         GAAAATGTGTTGGCAGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAGgtatatcttc ... attttgacagGAAAATGTGTTGGCAGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
EST: gi|4314076|gb|AI461195.1|AI461195
EST:     CAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAG                         GAAAATGTGTTGGCAGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC
genomic: CAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAGgtatatcttc ... attttgacagGAAAATGTGTTGGCAGAGTCTAGGATGATGATTCCTGACTGCCGCAAGCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGAGCTGCATTCTTATGAGAAGGAAGTTGAGAGAGAAGCTGCCAAAACAGCTGATATGACGGAAAAAGGAGCTGACCCCCATGATCTCAAGCAACAGgtatatcttctccctctgcatttgctttcaggtgatttgccacatcgggttatgtgttatttacttttctctgttaaaaaaaaattatgcaatttgatggtaaattttgttgagctgatttgcattttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA