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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCAGGCTAAGGAAATGTTAGATCATCTAGAAAGTGTTTTGGCCAATGAGCCTGTTGCTGTGAAGAGTGGCCAGTTTATTGTTGAAGTAAAACCCCAGgtatatataatttctgtatttgatttatcttagaagaaaatggctctttttatttactattgattaatattgaaatctcctttcgaaaaagctttccagg...

Basic information

species Glycine max
transcript GLYMA12G15500.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G15500.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os01g54560.2 (Oryza sativa), 5'ss of exon 3
TGCTCAGGCTAAGGAAATGTTAGATCATCTAGAAAGTGTTTTGGCCAATGAGCCTGTTGCTGTGAAGAGTGGCCAGTTTATTGTTGAAGTAAAACCCCAGgtatatataatttctgtatttgatttatcttagaagaaaatggctctttttatttactattgattaatattg--aaatctcctttcgaaaaagctttccagg-------
  | ||||| |||||  |  | |||||||| |||||||| || || ||||| |||||| |||| || ||||||||||| ||||||||||| ||||| |||||     || ||  | | ||| |||| ||    ||  |  |  |||   |||| | |||||  | |||||     ||     ||| |         |  |||       
CTCCCAGGCAAAGGAGTTACTTGATCATCTGGAAAGTGTATTAGCAAATGAACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAGgt-----tagttcatctgtttaatttctc----aaatacctttctcaacttatattctatttctaaatatctctgaacgaatttttgtctcgatcatagagggcacatt

upper sequence: GLYMA12G15500.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G118462_T01 (Zea mays), 5'ss of exon 2
TGCTCAGGCTAAGGAAATGTTAGATCATCTAGAAAGTGTTTTGGCCAATGAGCCTGTTGCTGTGAAGAGTGGCCAGTTTATTGTTGAAGTAAAACCCCAGgtatatataatttctgtattt--gatttatcttagaagaaaatggctctt---tttatttactattgattaatattgaaatctcctttcgaaaaagctttccagg
  | ||||| ||||| ||| | ||||| || ||||||||  | || ||||| || ||  |||| |||||||||||||| ||||||||||| ||||| |||||  ||  |  || |  ||||   ||   |  | ||||| |   | | ||    ||||    |  | ||| |    ||||    || | |   ||    |     
CTCACAGGCAAAGGAGATGCTTGATCACCTGGAAAGTGTACTAGCAAATGAACCAGTCTCTGTCAAGAGTGGCCAGTTCATTGTTGAAGTCAAACCACAGgttcattcatcttttacatttcaaatcctttcttgaagagatgtgtttttcaacttataagttcattatttacggcgaaaggggctctagctgaattggt-----

upper sequence: GLYMA12G15500.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv12s0028g01670.t01 (Vitis vinifera), 5'ss of exon 2
TGCTCAGGCTAAGGAAATGTTAGATCATCTAGAAAGTGTTTTGGCCAATGAGCCTGTTGCTGTGAAGAGTGGCCAGTTTATTGTTGAAGTAAAACCCCAGgtatatataatttctgt--atttgatttatcttagaa----gaaaatggctctttttatttactattgattaatattgaaatc--tcctttcgaaaaagctttccagg
  ||||||| ||||||||||| ||||||||||| ||||| || || ||||| ||||||||||| || ||||| || |||||||| ||||| || || |||||| ||||  |   | |  |||| ||  ||  |   |    ||||| |      |  |  || |  ||||  | ||  |  |   | | || | | ||          
CTCTCAGGCAAAGGAAATGTTGGATCATCTAGAGAGTGTATTAGCAAATGAACCTGTTGCTGTCAAAAGTGGTCATTTTATTGTAGAAGTTAAGCCTCAGgtacatatcgtgcatttcaatttcatccataattcgactctgaaaaagaaaaagtagaaataattctgatctaaatgaagtttgatacatttgcataaat--------

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|207800654|gb|GD774609.1|GD774609
EST:     CCAGTTTTATTTGTTGAAGTAAAACCCCAG                         GATGTGAGCAAAGGCTTAGTCGCCGAGAAGATATTTTCGTCAATGGACGGG
genomic: CCAG-TTTA-TTGTTGAAGTAAAACCCCAGgtatatataa ... tgttttgtagGATGTGAGCAAAGGCTTAGTCGCCGAGAAGATATTTTCGTCAATGGACGGG
EST: gi|7795612|gb|AW781009.1|AW781009
EST:     AGCCTGTTGCTGTGAAGAGTGGCCAGTTTATTGTTGAAGTAAAACCCCAG                         GATGTGAGCAAAGGCTTAGTCGCCGAGAAGATATTTTCGTCAATGGACGGG
genomic: AGCCTGTTGCTGTGAAGAGTGGCCAGTTTATTGTTGAAGTAAAACCCCAGgtatatataa ... tgttttgtagGATGTGAGCAAAGGCTTAGTCGCCGAGAAGATATTTTCGTCAATGGACGGG
EST: gi|5753714|gb|AI961001.1|AI961001
EST:     AGCCTGTTGCTGTGAAGAGTGGCCAGTTTATTGTTGAAGTAAAACCCCAG                         GATGTGAGCAAAGGCTTAGTCGCCGAGAAGATATTTTCGTCAATGGACGGG
genomic: AGCCTGTTGCTGTGAAGAGTGGCCAGTTTATTGTTGAAGTAAAACCCCAGgtatatataa ... tgttttgtagGATGTGAGCAAAGGCTTAGTCGCCGAGAAGATATTTTCGTCAATGGACGGG
EST: gi|151402400|gb|EV272213.1|EV272213
EST:     AGCCTGTTGCTGTGAAGAGTGGCCAGTTTATTGTTGAAGTAAA-CCCCAG                         GATGTGAGCAAAG-CTTAGTCGCCGAGA-GATATTT-CGTCA
genomic: AGCCTGTTGCTGTGAAGAGTGGCCAGTTTATTGTTGAAGTAAAACCCCAGgtatatataa ... tgttttgtagGATGTGAGCAAAGGCTTAGTCGCCGAGAAGATATTTTCGTCA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTCAGGCTAAGGAAATGTTAGATCATCTAGAAAGTGTTTTGGCCAATGAGCCTGTTGCTGTGAAGAGTGGCCAGTTTATTGTTGAAGTAAAACCCCAGgtatatataatttctgtatttgatttatcttagaagaaaatggctctttttatttactattgattaatattgaaatctcctttcgaaaaagctttccagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaagc