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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAGgtaagattgtcctgcacaattattaaaagtcaatttatgtccttgtatggattttgtgtctaatgtttgcttgatttttag

Basic information

species Glycine max
transcript GLYMA12G08670.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08670.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g57670.1 (Oryza sativa), 5'ss of exon 4
GTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAGgtaagattgtcctgcacaatta-----ttaaaagtcaatttatgtccttgtatggattttgtgtctaatgtttgcttgatttt-tag
||||||||||||||||| |||||||| |   ||||||||||| ||||||| ||||| |||   ||||||||||| ||||||||||| || ||||| ||| ||| || |   |   |  ||     |||    ||   ||||    ||   || | ||  |  | | | |||  |  ||| |  ||
GTAAAAGAAGAGGCACAGCAACTTGCCCGTGTTTTTGAAACTATTGGGGCATTCAAAGTGCCACGTAAAGGTGGGAAAGGAAAACAGATATTTGGGAGgcaagtttttatcgagtagatagttctttatgtatcgtcttat---tttacttgcacttaataacaagtttttcttctattctacag

upper sequence: GLYMA12G08670.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G096962_T01 (Zea mays), 5'ss of exon 4
GTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAGgtaagat-tgtcctgcacaatt-attaaaagtcaatttatgtccttgtatggattttgtgtctaatgtttgcttgatttttag-------------------------------------------------------------------------------------------------
||||||||||| || ||||||||||||| | ||||||||||  |||| ||||||||  |    || |||||||| ||||||||||| || ||||| ||| ||| | |    || |||||  ||||    |    |  ||||   |  |   | ||    || |    |       | | |                                                                                                  
GTAAAAGAAGACGCGCAACAACTTGCTCGAGTTTTTGAAACCATTGGCGCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttctaagttggacaatccattatttattctctcttgtctcaggctatctcttacagcttacccatctccatctctcatttcaaactctactttgtacacactgcaatctatagtgtcactatctgctgggtatagtcttactttcacttttctgacgatatcttttattgtacag

upper sequence: GLYMA12G08670.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G096962_T03 (Zea mays), 5'ss of exon 4
GTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAGgtaagat-tgtcctgcacaatt-attaaaagtcaatttatgtccttgtatggattttgtgtctaatgtttgcttgatttttag-----------------
||||||||||| || ||||||||||||| | ||||||||||  |||| ||||||||  |    || |||||||| ||||||||||| || ||||| ||| ||| | |    || |||||  ||||    |    |  ||||   |  |   | ||    || |    |       | | |                  
GTAAAAGAAGACGCGCAACAACTTGCTCGAGTTTTTGAAACCATTGGCGCTTTCAAACTCCCTCGCAAAGGTGGAAAAGGAAAACAGATCTTTGGGAGgcaagttctaagttggacaatccattatttattctctcttgtctcaggctatctcttacagcttacccatctccatctctcatttcaaactctactttgt

upper sequence: GLYMA12G08670.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0061g00770.t01 (Vitis vinifera), 5'ss of exon 4
GTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAGgtaagattgtcctgcacaattattaaaagtcaatttatgtccttgtatggattttgtgtctaatgtttgcttg-atttttag
|||||||||||||| |||||| | |||||||| |||||||||||||| |||||||||||||| || |||||||| |||||||| ||||| ||||||||||| | |    | || |||   | |  |   | ||| | |   | ||  ||     ||||| || |     |  |||   ||
GTAAAAGAAGAGGCCCAACAAATGGCTCTAATGTTTGAAACTGTTGGAGCTTTCAAGGTGAAACGCAAAGGTGGAAAAGGAAAGCAAATCTTTGGAAGgtaggttcaatcagctcaaagttaagcaactattttgtttgtctttagtgaccc-atgtctgatatgcatctatattgacag

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|11687696|gb|BF595372.1|BF595372
EST:     GCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAG                         TGTAACTGCTCAAGA
genomic: GCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAGgtaagattgt ... tgatttttagTGTAACTGCTCAAGA
EST: gi|23063991|gb|BU578764.1|BU578764
EST:     GCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAG                         TGTAACTGCTCAAGATCTTGTTGACATAATCAAGGCACAACTTCAAAG
genomic: GCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAGgtaagattgt ... tgatttttagTGTAACTGCTCAAGATCTTGTTGACATAATCAAGGCACAACTTCAAAG
EST: gi|151399558|gb|EV269429.1|EV269429
EST:     GCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAACCAAATTTTTGGAAG                         TGTAACTGCTCAAGATCTTGTTGACATAATCAAGGCACAACTTCAAAG
genomic: GCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAGgtaagattgt ... tgatttttagTGTAACTGCTCAAGATCTTGTTGACATAATCAAGGCACAACTTCAAAG
EST: gi|19452866|gb|BM954276.1|BM954276
EST:     GCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAG                         TGTAACTGCTCAAGATCTTGTTGACATAATCAAGGCACAACTTCAAAG
genomic: GCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAGgtaagattgt ... tgatttttagTGTAACTGCTCAAGATCTTGTTGACATAATCAAGGCACAACTTCAAAG
EST: gi|7796407|gb|AW781804.1|AW781804
EST:     GCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAG                         TGTAACTGCTCAAGATCTTGTTGACATAATCAAGGCACAACTTCAA
genomic: GCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAGgtaagattgt ... tgatttttagTGTAACTGCTCAAGATCTTGTTGACATAATCAAGGCACAACTTCAA
EST: gi|207746745|gb|GD719296.1|GD719296
EST:     GCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAG                         TGTAACTGCTCAAGATCTTGTTGACATAATCAAGGCACAACTTCAAAG
genomic: GCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAGgtaagattgt ... tgatttttagTGTAACTGCTCAAGATCTTGTTGACATAATCAAGGCACAACTTCAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAAAGAAGAGGCACAACAACTTGCTCTAATTTTTGAAACTGTTGGGGCTTTCAAGGTGAAGCGTAAAGGTGGTAAAGGAAAACAAATTTTTGGAAGgtaagattgtcctgcacaattattaaaagtcaatttatgtccttgtatggattttgtgtctaatgtttgcttgatttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG