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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAGgtatgatgaatgatcgtgctttttaaaaaatttctgttatgttttttaattgccctttcagttgcttcacacaatctccttcttatgtcttgttgattgt...

Basic information

species Glycine max
transcript GLYMA03G33080.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33080.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G53580.1 (Arabidopsis thaliana), 5'ss of exon 3
ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAGgtatgatgaatgatcgtgctttttaaaaaatttctgtt-atgttttttaattgccctttcagtt--gcttcacacaatctccttcttatgtcttgttgattgt----
||||||||||||||||| ||||||||||| |  ||  || || ||||||||||||| || || |  |||||||||            |   | || | |||| |||||| |   ||   | || |   || |||   |||| |   || ||      | | | |  ||| || |    
ATGTGTGGCAATGGAGTTCGATGCTTTGCTAGGTTCATTGCTGAGCTTGAGAATTTGCAGGGAAAACATAGgtatctc-------tatctgtattgagaaatatctgtttagacttgagagttccgagtttagtcaagcttgatgtaaccttaagtgtctatttatttgtttttgtag

upper sequence: GLYMA03G33080.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0040g02540.t01 (Vitis vinifera), 5'ss of exon 3
ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAGgtatgat----gaatgatcgtgctttttaaaaaatttctgtta-tgttttttaattgccctttcagttgcttcacacaatctccttcttatgtcttgttgattgt
|||||||| |||||||| ||||||||||||| |||  || |  ||||||| ||||| ||||||| ||| ||||||  |      || ||      || | ||    || || ||  | || ||  |||      || ||| |  ||| ||     ||  |   |    ||      
ATGTGTGGTAATGGAGTACGATGCTTTGCCAGATTCATTGCAGAGCTTGAAAATTTGCATGGGAAGCAAAGgtattgtttttatataattccatgttattaattgcttttgctaacggttcttgtttgaaa--acacttg-tagacataaaaaaattagtggattaaattacca--
















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|208205313|gb|GE004072.1|GE004072
EST:     TGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAG                         TTTTACCATTCATACTGGTGCTGGTCTGAT
genomic: TGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAGgtatgatgaa ... tactttgcagTTTTACCATTCATACTGGTGCTGGTCTGAT
EST: gi|120532038|gb|EH260171.1|EH260171
EST:     TGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAG                         TTTTACCATTCATACTGGTGCTGGTCTGATTATTCCTGAAGTCTTGGAGGA
genomic: TGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAGgtatgatgaa ... tactttgcagTTTTACCATTCATACTGGTGCTGGTCTGATTATTCCTGAAGTCTTGGAGGA
EST: gi|193479421|gb|FK444206.1|FK444206
EST:     TGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAG                         TTTTACCATTCATACTGGTGCTGGTCTGATTATTCCTGAAGTCTTGGAGGA
genomic: TGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAGgtatgatgaa ... tactttgcagTTTTACCATTCATACTGGTGCTGGTCTGATTATTCCTGAAGTCTTGGAGGA
EST: gi|9986785|gb|BE660893.1|BE660893
EST:     TGCTTTGCCAAATTTGGTTCTCAGCTTGAGAATTTACATGGGANGCATAG                         NTTTACCATTCATACTGGTGCTGGGCTGAATATT
genomic: TGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAGgtatgatgaa ... tactttgcagTTTTACCATTCATACTGGTGCTGGTCTGATTATT
EST: gi|298175599|gb|HO015118.1|HO015118
EST:     TGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAG                         TTTTACCATTCATACTGGTGCTGGTCTGATTA
genomic: TGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAGgtatgatgaa ... tactttgcagTTTTACCATTCATACTGGTGCTGGTCTGATTA
EST: gi|192298876|gb|FG987621.1|FG987621
EST:     TGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAG                         TTTTACCATTCATACTGGTGCTGGTCTGATTATTCCTGAAGTCTTGGAGGA
genomic: TGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAGgtatgatgaa ... tactttgcagTTTTACCATTCATACTGGTGCTGGTCTGATTATTCCTGAAGTCTTGGAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAGAATTTACATGGGAGGCATAGgtatgatgaatgatcgtgctttttaaaaaatttctgttatgttttttaattgccctttcagttgcttcacacaatctccttcttatgtcttgttgattgt

- - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccttc