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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatttgcattgatctttgctacatgtttgtttgggtgcttctctctccctctgaatgattataaccgtgcttataattttcagGTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCATTCATGTGCTTTGGAATTGGTTTTATTTTAAACACAATTGCTATATTCTATGG

Basic information

species Glycine max
transcript GLYMA08G20100.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 9
------gtaagaatttgcattgatctttgctacatgtttgtttgggtgcttctctctccctctgaatgattat---aaccgtgctta---taattttcagGTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCATTCATGTGCTTTGGAATTGGTTTTATTTTAAACACAATTGCTATATTCTATGG
       |  ||| || |    || |        |  |   ||   |  | |    ||    || ||| || |   ||||||  ||    ||  |  |||||||||| ||||| ||  | ||||||||||||||||| || || |||||| ||||||||| |||||| ||| || | || ||||||||||| |||||  |
ttttttttttgaagtttctagaatttgcatgttgtcatatattatattttcccacttcatgatgtatggttttttgaaccgtaatttccttacatggcagGTAAAAACTGGATAAAGGCTATGATCCTTACAGCATCCCTATTTCCATTCTTGTGCTTTGCAATTGGCTTTGTTCTGAATACAATTGCTATCTTCTACCG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 8
gtaagaatttgcat-tgatctttgctacatgtttgtttgggtgcttctctctccctctgaatgattataa--ccgtgcttataattttcagGTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCATTCATGTGCTTTGGAATTGGTTTTATTTTAAACACAATTGCTATATTCTATGG
||| |   ||   | | || |    |  |  | | |     |  |||| |      || | |  || |||  || |    |  |    |||| ||||| ||||| ||  | |||  | | ||||||||||| |||||||| |||||||||||||||||  |  |  | ||||| ||||||||         
gtatgggcttatttatcatgtaaaattgaactgtatacctatagttctataaggtgctcagttgttttaaatccttttggagGAGGAGCAGGGAAAAACTGGATCAAGGCAATGGCCATGACAGCATCACTTTTCCCATTTATGTGCTTTGGAATTGGCCTGGTGCTTAACACTATTGCTAT---------

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagaatttgcattgatctttgctacatgtttgt-ttgggtgcttctctctccctctgaatgattataaccgtgcttataattttcagGTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCATTCATGTGCTTTGGAATTGGTTTTATTTTAAACACAATTGCTATATTCTATGG
||| ||  || |     |    |   |      || ||   | | |||||  |  |   | | |||  ||   || ||    | |||||||||| ||||||| || | |||| |||| || || || || ||||| ||  ||||||| |||||||| ||| |  ||||||||||||| |||||||||||
gtatga-cttactcgacttggcggacccctccagtgttactttcctctctaactattcaagtaatttaaatgctggtt----tattcagGTAAACATTGGATCAAGTGCATGGTCCTCACGGCTTCTCTCTTCCCCTTTTTGTGCTTCGGAATTGGCTTTCTCCTAAACACAATTGCCATATTCTATGG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------------------------------------------------------gtaagaatttgcattgatctttgctacatgtttgtttgggtgcttctctctccctctgaatgattataaccgtgcttataattt-tcagGTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCATTCATGTGCTTTGGAATTGGTTTTATTTTAAACACAATTGCTATATTCTATGG
                                                                                                ||| ||||   ||||| | | ||||     ||| |  ||| ||   |||    || ||| || || ||    ||   |  || ||||||||||  |||||||| || ||||| || || |||||||| || ||||| ||||||||||| ||||| ||  | || || ||||||||||||||||||||
gtatgtacttcatccgtcaactggtcgatggctaagtttcttgtttttctgggcttccttccatatcttttgtgctttttttgggttatatttaacaagtatttc--ttgatatgttctactcaactgtctttgtgattgcttctggtgctaaattat-atcacttctctgtcatcttgtcagGTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTATGTGCTTTGGGATTGGGTTCTTGTTGAATACAATTGCTATATTCTATGG

upper sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 9
-----------------------------------------------------------------------------------------gtaagaatttgcattgatctttgctaca--tgtttgtttgggtgcttctctctccctctgaat-------gattataaccgtgcttataattttcagGTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCATTCATGTGCTTTGGAATTGGTTTTATTTTAAACACAATTGCTATATTCTATGG
                                                                                          |   | | |  ||  |||| | ||| |  || |  |||      |  | ||  | | ||  |       | |||| || |||  ||   || ||||||||||  ||||| || || ||||| || || |||||||| ||||| || ||||||||||| |||||||| || || |||||||||||||||||||||||
gtaagtaatttgtacattatgttgcctcactcttagtcttctgtcaccccctaaatttcatgtacgaaaggcatggcctgtttttgattcttttattgtcaatgaatctcttctataaatggtcatttcctctgtcttatcagcatttgtttactggtggcttattactgtgtctac--ttgtcagGTAAAAGCTGGATAAAGTCAATGATACTCACTGCATCACTTTTCCCGTTTATGTGCTTTGGGATTGGTTTCATCTTGAACACAATTGCTATATTCTATGG

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|192331779|gb|FK024883.1|FK024883
EST:     ATCTTTCATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGTAATGGGG                         GTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCTTTCA
genomic: ATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGGgtaagaattt ... taattttcagGTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCATTCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgggtgcttctctctccctctgaatgattataaccgtgcttataattttcagGTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCATTCATGTGCTTTGGAATTGGTTTTATTTTAAACACAATTGCTATATTCTATGG
                              ttataac  putative branch site (score: 2)
                                                ttttc  putative PPT
                                          ttataattttca  TA-rich tract