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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatggcctacactgcagttttatctattttcctttatacatagatgccctcaaatctcattgccttctgtttgattcttttttctttttttaaaattcagTATGGCAGAAGCTGGAAGAGGAGAACACTGATTTCTTTAGGGCCTACTATATCAGGCTAAAATTAAAAAGGCAAATACTTTTGTTCAATCATTTGCTTGA

Basic information

species Glycine max
transcript GLYMA19G44420.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G44420.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g12080.3 (Oryza sativa), 3'ss of exon 4
aatggcctacactgcagttttatctattttcctttatacatagatgccctcaaatctcattgccttctgtttgattcttttttct-ttttttaaaattcagTATGGCAGAAGCTGGAAGAGGAGAACACTGATTTCTTTAGGGCCTACTATATCAGGCTAAAATTAAAAAGGCAAATACTTTTGTTCAATCATTTGCTTGA
       |  | || |  |  | |  |     ||  || |||  | |  |    | | | |   | ||| |   || | |||  |  | ||| |  ||||||||||||||| || ||||| |||||| |||| |||||| | || ||||||||  || | ||||| |||||||| ||  | |||||||| ||||| ||  |
tgctatgtctattgtatataaagcc-tccagattgctatatatgtccattagccttttaatttatgctgctcatttttgtttgatactctttgatgttcagTATGGCAGAAACTTGAAGAAGAGAACTCTGAATTCTTTCGTGCTTACTATATACGGTTGAAATTGAAAAGGCAGATTATCTTGTTCAACCATTTACTGCA

upper sequence: GLYMA19G44420.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G154221_T01 (Zea mays), 3'ss of exon 4
---aatggcctacactgcagttttatctattttcctttatacatagatgccctcaaatctcattgccttctgtttgattcttttttctttttttaaaattcagTATGGCAGAAGCTGGAAGAGGAGAACACTGATTTCTTTAGGGCCTACTATATCAGGCTAAAATTAAAAAGGCAAATACTTTTGTTCAATCATTTGCTTGA
   ||    |     |  |  |||    |  ||    |   ||    ||  || |  ||| | | |      |||  ||   || | | ||| |    ||||||||||||||| || ||||| |||||| | || ||||||||||| ||||||||| || | ||||| ||| |||||||  | ||||||||||||||  |  |
acaaacaaacatttttatatgttttctgaacttaaccttcgcaatactgatctgagctcttaattctactcattttgtttaattctatctttatg---ttcagTATGGCAGAAACTCGAAGAAGAGAACTCCGAGTTCTTTAGGGCTTACTATATCCGGTTGAAATTGAAACGGCAAATCATCTTGTTCAATCATTTATTGCA

upper sequence: GLYMA19G44420.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G816784_T02 (Zea mays), 3'ss of exon 4
aatggcctacactgcagttttatctattttcctttatacatagatgccct-caaatctcattgcctt-ctgt-ttgattcttttt--tctttttttaaaattcagTATGGCAGAAGCTGGAAGAGGAGAACACTGATTTCTTTAGGGCCTACTATATCAGGCTAAAATTAAAAAGGCAAATACTTTTGTTCAATCATTTGCTTGA
     |  |||    | |||||| |  ||||     |  | |  |||  | |  |||| |   | |   |||  | ||| | |||  | || | ||    ||||||||||||||| || ||||| || ||| | || ||||||||||| ||||||||  || | || || |||||||| ||  | ||||||||||||||  |  |
----acaaacaa-atatttttatatgctttctaagctcaacatctgcaatacctatctgagctcttaattgtactcattttgtttaatgttctctttgtgttcagTATGGCAGAAACTTGAAGAAGAAAACTCCGAGTTCTTTAGGGCTTACTATATACGGTTGAAGTTGAAAAGGCAGATCATCTTGTTCAATCATTTATTGCA

upper sequence: GLYMA19G44420.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G61700.1 (Arabidopsis thaliana), 3'ss of exon 4
----aatggcctacactgcagttttatctattttcctttatacatagatgccctcaaatctcattgccttctgtttgattcttttttctttttttaaaattcagTATGGCAGAAGCTGGAAGAGGAGAACACTGATTTCTTTAGGGCCTACTATATCAGGCTAAAATTAAAAAGGCAAATACTTTTGTTCAATCATTTGCTTGA
     |||   || | ||     ||||    ||  |    |  | | |||   | |||||||  |   |||||  |     |||| | || | |   || ||||| ||||||||  ||||||| || ||| | || || || ||||| || ||||| ||||| ||| | || | ||||||| ||||||||||||||||||||||
aatgcatgttatatattgtttagttatagcattagcaacgtgaa-acatgaaatgaaatctctat---ttctgactctcctttttattttatgtgtgaaatcagTTTGGCAGAAATTGGAAGAAGAAAACGCAGACTTTTTCAGGGCATATTATATAAGGCTGAAACTGAAGAAGCAAATAATTTTGTTCAATCATTTGCTTGA

upper sequence: GLYMA19G44420.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g00990.t01 (Vitis vinifera), 3'ss of exon 4
----aatggcctacactgcagttttatctattttcctttatacatagatgccctcaaatct-cattgccttctgtttgattcttttttctttttttaaaattcagTATGGCAGAAGCTGGAAGAGGAGAACACTGATTTCTTTAGGGCCTACTATATCAGGCTAAAATTAAAAAGGCAAATACTTTTGTTCAATCATTTGCTTGA
    |   || ||  ||||  |  ||  |||  |  ||  |      ||||   |||     |||||  ||||| |    |||| ||||||| ||   || ||||||||||||||| ||||||| || ||  ||||||| || |||||||| || || ||  ||||||| || |  |||||  ||||||| ||||||||||||||
tttgagaagctta-gctgcc-taataaatatgatatttgtttgtctaatgcttccaagcaagcattgttttctgatgtcctcttctttctttgtt---aactcagTATGGCAGAAGTTGGAAGAAGAAAATGCTGATTTTTTCAGGGCCTATTACATAAGATTAAAATTGAAGAAACAAATCATTTTGTTTAATCATTTGCTTGA

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|192296878|gb|FG990239.1|FG990239
EST:     CAAAACACTCTTCGCTCGGGCAAAGATAGATCCTGGATTTACAACTCTGG                         TATGGCAGAAGCTGGAAGAGGAGAACACTGATTTCTTTAGGGCCTACTATA
genomic: CAAAACACTCTTCGCTCGGGCAAAGATAGATCCTGGATTTACAACTCTGGgtagccatct ... taaaattcagTATGGCAGAAGCTGGAAGAGGAGAACACTGATTTCTTTAGGGCCTACTATA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccctcaaatctcattgccttctgtttgattcttttttctttttttaaaattcagTATGGCAGAAGCTGGAAGAGGAGAACACTGATTTCTTTAGGGCCTACTATATCAGGCTAAAATTAAAAAGGCAAATACTTTTGTTCAATCATTTGCTTGA
                       gtttgat  putative branch site (score: 5)
         tctcattgccttctgt  CT-rich tract
                      tgtttgattctttttt  TA-rich tract