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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcttagaagatcttatttgtttttttcttttatgcacaagaaattctctcctctgatctgaagcacgtgtttttttttcttctactttgtctttcataacgcagATATCACGCAATATTACAACAAATGAAATGGCAAATGCAATGCGGTATAGTTACCTCAGAGGTCCAGGTGGTAGATTTAGAAACCCATATGATCATGGTA

Basic information

species Glycine max
transcript GLYMA17G11600.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g09130.1 (Oryza sativa), 3'ss of exon 12
gtatgtcttagaagatcttatttgtttttttcttttatgcacaagaaattctctcctctgatctgaagcacgtgtttttttttcttctactttgtctttcataacgcagATATCACGCAATATTACAACAAATGAAATGGCAAATGCAATGCGGTATAGTTACCTCAGAGGTCCAGGTGGTAGATTTAGAAACCCATATGATCATGGTA
 | | | ||      || |     || |  |    |    | |     ||    |      | | ||  || |   | |   || | || ||  ||||       |||||||||  | ||| | ||||||||||| ||||||||||| ||| |||||||||| |||||||| ||||||||  |||| ||||| |||| ||| |||||  
-tgtttttttctcagtccttgcaattatcattccctgcttata-----tttgggctctatttttaaattacat---tgtcaatcatttatttcttcttatcccttgcagATATCCAGGAATTTAACAACAAATGAGATGGCAAATGCCATGAGGTATAGTTATCTCAGAGGCCCAGGTGGCCGATTCAGAAATCCATTTGACCATGGGG

upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g43680.1 (Oryza sativa), 3'ss of exon 12
gtatgtcttagaagatcttatttgtttttttcttttatgcacaagaaattctctcctctgatctgaagcacgtgtttttttttcttctactttgtctttcataacgcagATATCACGCAATATTACAACAAATGAAATGGCAAATGCAATGCGGTATAGTTACCTCAGAGGTCCAGGTGGTAGATTTAGAAACCCATATGATCATGGTA
       |    | | ||| ||     |   |       |   || |    | |  |||| ||||    | |   | ||  | | |    |   |||  |||   ||||||| |    || ||||||||||| || ||||||||| | ||| | || ||||| || |||||||||||||| ||||| |||||||||| ||| |||||  
-----ggtagctataactttttcagaatggacacgaggacttgaggagcattttt-tctgttctgttttatgacgtgttcatgccttacttccatctcccat---gcagATAGCGAAGAACATTACAACAAACGAGATGGCAAATTCCATGAGATACAGTTATCTAAGAGGTCCAGGTGGAAGATTCAGAAACCCATTTGACCATGGAG

upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G409934_T01 (Zea mays), 3'ss of exon 6
---gtatgtcttagaagatcttatttgtttttttcttttatgcacaagaaattctctcctctgatctgaagcacgtgtttttttttcttctactttgtctttcataacgcagATATCACGCAATATTACAACAAATGAAATGGCAAATGCAATGCGGTATAGTTACCTCAGAGGTCCAGGTGGTAGATTTAGAAACCCATATGATCATGGTA
   | || |  ||  ||    || |   | ||||| ||  ||||     ||  | ||  | ||  |      |    || ||  |  |||||| |||            ||||||||  | || |||||||||||||| ||||||||| | ||  |||| ||||||||||| || ||| |||| ||||| ||||| |||||||| |||||  
actgcatctgatatcaggcactactgactcttttccttcctgcatctttaacccacttttatgcaccatctgatagtttcttgctatttctaccttg------------cagATATCCAGGAACATTACAACAAATGAGATGGCAAATACCATTAGGTACAGTTACCTCAGGGGACCAAGTGGCAGATTCAGAAATCCATATGACCATGGGC

upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G024437_T02 (Zea mays), 3'ss of exon 11
gtatgtcttagaagatcttatttgtttttttcttttatgcacaagaaattctctcctctga------tctgaagcacgtgtttttttttcttctactttgtctttcataacgcagATATCACGCAATATTACAACAAATGAAATGGCAAATGCAATGCGGTATAGTTACCTCAGAGGTCCAGGTGGTAGATTTAGAAACCCATATGATCATGGTA
               |    |   |   ||  || ||   | |||  || |   | |||        | || |    |    |    |  | |   | |  | || |    ||||||| || | || |||||||||||||| ||||||||| | ||| | |||   || |||||||| |||||||| ||||| || ||||| ||||||||||| |
---------------ttcattccatcaattcattatacataaaaggcatacctgcatctacctactctttgtactgtgctcatgcagtcatgcctttcttacatttaacttgcagATAGCAAGGAACATTACAACAAATGAGATGGCAAATTCCATGAGATATGCATATCTCAGAGGCCCAGGTGGCAGATTCAGGAACCCGTATGATCATGGGA

upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatgtcttagaagatcttatttgtttttttcttttatgcacaagaaattctctcctctgatctgaagcacgtgtttttttttcttctactttgtctttcataacgcagATATCACGCAATATTACAACAAATGAAATGGCAAATGCAATGCGGTATAGTTACCTCAGAGGTCCAGGTGGTAGATTTAGAAACCCATATGATCATGGTA
       |    || |   | |   |   |    |     |   ||  |||    |   |   |    | | |  |     | | |   |  | | || | | ||  |||||||| | || || || |||||||||||||| || ||  ||||||| || ||||| ||||||||||||||| | ||||| || || |||||||  ||  
-------tccagagctaaaactcactaagtagactagattattcgattttcatggcgtggtgttttgcctcatcctgaagatccattctccctattttcccttac--agATATCAAGGAACATAACCACAAATGAAATGGCCAACGCCCTGCGGTACAGCTACCTAAGAGGTCCAGGTGGTCGGTTTAGGAATCCTTATGATCTCGGGT

upper sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 12
gtatgtcttagaagatcttatttgtttttttcttttatgcacaagaaattctctcctc---tgatctgaagcacgtgtttttttttcttctactttgtctttcataacgcagATATCACGCAATATTACAACAAATGAAATGGCAAATGCAATGCGGTATAGTTACCTCAGAGGTCCAGGTGGTAGATTTAGAAACCCATATGATCATGGTA
            ||  ||| ||   |  ||||   |    | |  |  ||   |  |    | || ||    | |||   |  |   ||   |    |  ||  |   ||||||||| |||||||||||||||||||||||||| ||||| ||||| ||||| || || ||||| || |||||| | || || ||||||||||||| |||  
------------agtactttttccatcctttcagctgccaatagaatcttaattgttgaagttatatgttaaaagtgagatgctgattttggcaactttctttttgctgcagATATCGCGCAATATTACAACAAATGAAATGGCTAATGCTATGCGCTATAGCTATCTTAGAGGGCCTGGTGGTCGGTTCAGGAACCCATATGATCGTGGGT

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|23731604|gb|BU763933.1|BU763933
EST:     TTTTCCTCTTCTTTGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAG                         ATATCACGCAATATTACAACAAATGAAATGGCAAATGCAATGCGGTATAGT
genomic: TTTTCCTCTTCTTTGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAGgtatgtctta ... cataacgcagATATCACGCAATATTACAACAAATGAAATGGCAAATGCAATGCGGTATAGT
EST: gi|254317846|gb|GR826830.1|GR826830
EST:     TTTT-CTCTTCTTTGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAG                         ATATCACGCAATATTACAACAAATGAAATGGCAAATGCAATGCGGTATAGT
genomic: TTTTCCTCTTCTTTGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAGgtatgtctta ... cataacgcagATATCACGCAATATTACAACAAATGAAATGGCAAATGCAATGCGGTATAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctctgatctgaagcacgtgtttttttttcttctactttgtctttcataacgcagATATCACGCAATATTACAACAAATGAAATGGCAAATGCAATGCGGTATAGTTACCTCAGAGGTCCAGGTGGTAGATTTAGAAACCCATATGATCATGGTA
                                            tcataac  putative branch site (score: 2)
                cgtgtttttttttctt  CT-rich tract
                    tttttttttcttcta  TA-rich tract