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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtcattgcgacacataacaatccatgtttcttcatcttgggttgattttgactgatttttatgtcctactactacaattaccttgct...

Basic information

species Glycine max
transcript GLYMA09G28980.2
intron # 4
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28980.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 5'ss of exon 4
CAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtcattgcgacacataacaatccatgtttcttcatcttgggttgattttgactgatttttatgtcc-tactactacaattaccttgct-
|||||||||| |||| || || ||||| ||||||||||| ||||| || ||||| || || || || || ||||| || || ||||||||||| ||||||||||||| || |  |  |     |  ||     | |||  | |    || ||     |     |  || | |||  ||  ||   ||  ||  |   |  | 
CAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctcttcttttagtcatagcttatgttt-tgcatagtacagtttcatgaaaaaaaaa-aagggactattagctcaatatagctcaaaccagtcttatg

upper sequence: GLYMA09G28980.2 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 4
CAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtcattgcgacacataacaatccatgtttcttcatcttgggttgattttgactgattt---ttatgtcctactactacaattaccttgct------------------------------------------------------------------------------------------
||| |||||| | ||||| || ||||||||||||||||| || || |||||||| ||||| || ||||  ||||| || |||||||||||||| |||||||||||||||  |  ||||    | || |  |  | | ||||      |    | |    | ||| | || |   | |  |     | ||  ||     | ||                                                                                           
CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctttattaatcatcaaca-actttgcttttcctgttatacagttaatgatacggtctgattaatatggttcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac

upper sequence: GLYMA09G28980.2 (Glycine max), 5'ss of exon 4
lower sequence: AT1G73350.2 (Arabidopsis thaliana), 5'ss of exon 4
CAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtcattgcgaca-cataacaat-----ccatgtttcttcatcttgggttgattttgactgatttttatgtcctactactacaattaccttgct
 || || ||| |||||||||| ||||| || |||||||| ||||| ||||||||||| || ||| | || ||||| |||||||| |||||||| ||||| |||||||||  |      |  || | ||| |   |     | | |||  || || |    |||   | ||    ||||| |   ||      || || |  |  | 
TAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGGAAGATGCAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAAatatcctttcttaaatgctcagatatcatgattttgagcactaagttatttgatatatacttg-cctagatgtttttttgtaatctttcttgaccat-atatcac-

upper sequence: GLYMA09G28980.2 (Glycine max), 5'ss of exon 4
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 5'ss of exon 4
CAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtcattgcgacacataacaatccatgtt----tcttcatcttgggttgattttgactgatttttatgtcctactactacaattaccttgct--------
            ||| |||||||| ||||| ||||| || ||||||||||||||||||||  | || ||||| || || || || |||||||||||||||||||||||| |||  | ||  ||     |||  |  |  ||    |     | |      | ||  ||  | |  | |||| ||   |    ||||   ||||         
------------ACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGCATTTAAGATATCCTTTCGTgtgcctttagatttgcaactgtgtacattagggtggctgtgtcattggggttgagatagctcgtaatgttctggcatgcaaattttattgcaaaaaaaag

upper sequence: GLYMA09G28980.2 (Glycine max), 5'ss of exon 4
lower sequence: PP1S402_46V6.1 (Physcomitrella patens), 5'ss of exon 4
-------CAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtca--ttgcgacacataacaatccatgtttcttcatcttgggttgattttgactgatttttatgtcctactactacaattaccttgct
        ||||||||| | |||||  | ||||||||||||||||| ||||||||||| || ||  | | ||| || ||||| |||||||| || || || ||||| |||||||| ||   |    ||   | |  |  | |||  || | |   |||     | |||| |     | | | | |   |  |  || |           
CATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaatatccttatgacatttatttattatatttttctatcagtgctacaatatcaaaattggattatctaaaaatgtca-gaagtgatggtagag----------

upper sequence: GLYMA09G28980.2 (Glycine max), 5'ss of exon 4
lower sequence: EFJ15111 (Selaginella moellendorffii), 5'ss of exon 4
-------CAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttt-tgtggtcattgcgac-acataacaatccatgtttcttcatcttgggttgattttgactgatttttatgtcctactactacaattaccttgct
       ||| |||||||| || || |||||||| || |||||||||||||||||||| ||  |  |   | |  |  | || ||   ||| |||| ||| ||||||||||||||       |     || | |  |     ||| || ||  ||  ||||    || |||  | |                                 
CTCTTGACAGCGATGATCTTCTCTACCTCAAAGAACAGATGGAAGCCGAGGAGGATGCCGAGAGGgtgaggaggagatcagagaagaaggcgtttgatgcgtttaagatatccttcacacttttgagacggctatctctttttccgtgattgatctccttgacgcgagttttccag---------------------------------

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|51335221|gb|CO979087.1|CO979087
EST:     CAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAG                         AGAGCTGCAAGTTTAGCAGATTCTTCACCTGCATCAGTACCACTGGCATTT
genomic: CAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatcctttt ... cagtgaatacAGAGCTGCAAGTTTAGCAGATTCTTCACCTGCATCAGTACCACTGGCATTT
EST: gi|120532801|gb|EH260934.1|EH260934
EST:     CAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAG                         AGAGCTGCAAGTTTAGCAGATTCTTCACCTGCATCAGTACCACTGGCATTT
genomic: CAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatcctttt ... cagtgaatacAGAGCTGCAAGTTTAGCAGATTCTTCACCTGCATCAGTACCACTGGCATTT
EST: gi|18040197|gb|BM308491.1|BM308491
EST:     CAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAG                         AGAGCTGCAAGTTTAGCAGATTCTTCACCTGCATCAGTACCACTGGCATTT
genomic: CAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatcctttt ... cagtgaatacAGAGCTGCAAGTTTAGCAGATTCTTCACCTGCATCAGTACCACTGGCATTT

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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtcattgcgacacataacaatccatgtttcttcatcttgggttgattttgactgatttttatgtcctactactacaattaccttgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC