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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcttagaaggtcttatttagtttttttcttttgtgcacaagaagttctctactttgatctgaagcacgtgccttttttttttttccctactactttcatgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAATTACCTCAGAGGTCCAGGTGGTAGATTCAGAAACCCATATGATCATGGTA

Basic information

species Glycine max
transcript GLYMA13G23230.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g09130.1 (Oryza sativa), 3'ss of exon 12
gtatgtcttagaaggtcttatttagtttttttcttttgtgcacaagaagttctctactttgatctgaagcacgtgccttttttttttttccctactactttcatgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAATTACCTCAGAGGTCCAGGTGGTAGATTCAGAAACCCATATGATCATGGTA
 | | | ||     ||| | |  | || |  |    ||   | |    |  ||||| ||| |  | |     ||   |  ||| ||| | | ||   |||        ||||||||  | ||| | ||||||||||| |||||||||||  || |||||| ||| |||||||| ||||||||  |||||||||| |||| ||| |||||  
-tgtttttttctcagtcct-tgcaattatcattccctgcttatatttggg-ctctatttttaaattacat-tgtcaatcatttatttcttcttatccctt-------gcagATATCCAGGAATTTAACAACAAATGAGATGGCAAATGCCATGAGGTATAGTTATCTCAGAGGCCCAGGTGGCCGATTCAGAAATCCATTTGACCATGGGG

upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os06g43680.1 (Oryza sativa), 3'ss of exon 12
gtatgtcttagaaggtcttatttagtttttttcttttgtgcacaagaagttc-------tctactttgatctgaagcacgtgccttttttttttttccctactactttcatgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAATTACCTCAGAGGTCCAGGTGGTAGATTCAGAAACCCATATGATCATGGTA
             |||    | ||  |||||     ||  ||| || | ||        | |  | || ||||    | |  | | ||  |   || | | |  ||  ||||   |||||| |    || || |||||||| || ||||||||| |  || | || | ||| || |||||||||||||| |||||||||||||||| ||| |||||  
-------------ggtagc-tataactttttcagaatggacacgaggacttgaggagcattttttctgttctgttttatg-acgtgttcatgccttacttccatctcccatg---cagATAGCGAAGAACATTACAACAAACGAGATGGCAAATTCCATGAGATACAGTTATCTAAGAGGTCCAGGTGGAAGATTCAGAAACCCATTTGACCATGGAG

upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G024437_T02 (Zea mays), 3'ss of exon 11
gtatgtcttagaaggtcttatttagtttttttcttttgtgcacaagaagttctctactttgatctgaagcacgtgcctttttt------ttttttccctactactttcatgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAATTACCTCAGAGGTCCAGGTGGTAGATTCAGAAACCCATATGATCATGGTA
                 | |||   |   ||  || |    | |||   | | || | |  | ||       || |  |  |       |  |  |  |  ||| || |     |||||| || | || || ||||||||||| ||||||||| |  || | |||   || |||||||| |||||||| |||||||| ||||| ||||||||||| |
----------------ttcattccatcaattcattatacataaaaggcatac-ctgcatctacctactctttgtactgtgctcatgcagtcatgcctttcttacatttaacttgcagATAGCAAGGAACATTACAACAAATGAGATGGCAAATTCCATGAGATATGCATATCTCAGAGGCCCAGGTGGCAGATTCAGGAACCCGTATGATCATGGGA

upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G087806_T01 (Zea mays), 3'ss of exon 12
gtatgtcttagaaggtcttatttagtttttttcttttgtgcacaagaagttctctactttgatctgaagcacgtgccttttttttttttccctactactttcatgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAATTACCTCAGAGGTCCAGGTGGTAGATTCAGAAACCCATATGATCATGGTA
         | |       |||   |   |   || |      ||||  | |     | |  |||   |   || |  |  |  |   |  || | |  |   |    |||||| || | || || ||||||||||| ||||||||  |  || | |||   ||||||||||| |||||||| |||||||| || || ||||||||||| |
---------atagctatccattccatcaatccattatacatgaaagacatacctgcatatactctactgtttgtactgtgctcatgccttgcttccatatcact--tgcagATAGCAAGGAACATTACAACAAATGAGATGGCAAACTCCATGAGATATGCATACCTCAGAGGCCCAGGTGGCAGATTCAGGAATCCGTATGATCATGGGA

upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G409934_T01 (Zea mays), 3'ss of exon 6
---gtatgtcttagaaggtcttatttagtttttttcttttgtgcacaagaagttctctactttgatctgaagcacgtgccttttttttttttccctactactttcatgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAATTACCTCAGAGGTCCAGGTGGTAGATTCAGAAACCCATATGATCATGGTA
   | || |  ||  |||   || | | | |||| |||   ||||        ||| ||      | | | ||||       | |  |  || | | ||| ||  |     ||||||||  | || || ||||||||||| ||||||||| |  |  |||| | ||||||||| || ||| |||| ||||||||||| |||||||| |||||  
actgcatctgatatcaggcactactgactcttttccttcc-tgca--------tctttaacccacttttatgcac-----catctgatagtttcttgctatttctaccttgcagATATCCAGGAACATTACAACAAATGAGATGGCAAATACCATTAGGTACAGTTACCTCAGGGGACCAAGTGGCAGATTCAGAAATCCATATGACCATGGGC

upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 13
lower sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 12
-gtatgtcttagaaggtcttatttagtttttttcttttgtgcacaaga---agttctctactttgatctgaagcacgtgccttttttttttttccctactactttcatgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAATTACCTCAGAGGTCCAGGTGGTAGATTCAGAAACCCATATGATCATGGTA
   |   || | |    || | |    |   || ||   |   || |     ||  | | | |    |||||| |       |   | |||| || |||              |||||||| | || || || |||||||||||||| || || |||||||| |  ||||| ||||||||||||||| | || || || || |||||||  ||  
tccagagctaaaactcactaagtagactagattattcgattttcatggcgtggtgttttgcctcatcctgaag-atccattctccctattttcccttac--------------agATATCAAGGAACATAACCACAAATGAAATGGCCAACGCCCTGCGGTACAGCTACCTAAGAGGTCCAGGTGGTCGGTTTAGGAATCCTTATGATCTCGGGT

upper sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 12
gtatgtcttagaaggtcttatttagtttttttcttttgtgcacaagaagttctctactt---tgatctgaagcacgtgccttttttttttttccctactactttcatgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAATTACCTCAGAGGTCCAGGTGGTAGATTCAGAAACCCATATGATCATGGTA
              ||  | |||   |  ||||   ||   | |  |  ||   |  |    | || ||    | |||   |  |  ||||  |  |||   ||  ||   |||||||| |||||||| ||||||||||||||||| |||||  |||| ||||  || || ||||| || |||||| | ||||| ||||||||||||| |||  
-------------agtactttttccatcctttcagctgccaatagaatcttaattgttgaagttatatgttaaaagtgagatgctgattttggca-actttctttttgctgcagATATCGCGCAATATTACAACAAATGAAATGGCTAATGCTATGCGCTATAGCTATCTTAGAGGGCCTGGTGGTCGGTTCAGGAACCCATATGATCGTGGGT

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|15663023|gb|BI700394.1|BI700394
EST:     TTTTCCTCTTCTTCGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAG                         ATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAAT
genomic: TTTTCCTCTTCTTCGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAGgtatgtctta ... catgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAAT
EST: gi|23054538|gb|BU577626.1|BU577626
EST:     TTTTCCTCTTCTTCGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAG                         ATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAAT
genomic: TTTTCCTCTTCTTCGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAGgtatgtctta ... catgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAAT
EST: gi|15814634|gb|BI786909.1|BI786909
EST:     TTTTCCTCTTCTTCGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAG                         ATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAAT
genomic: TTTTCCTCTTCTTCGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAGgtatgtctta ... catgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAAT
EST: gi|298180896|gb|HO022335.1|HO022335
EST:     TTTTCCTCTTCTTCGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAG                         ATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAAT
genomic: TTTTCCTCTTCTTCGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAGgtatgtctta ... catgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAAT
EST: gi|58018760|gb|CX705502.1|CX705502
EST:     TTTTCCTCTTTTTCGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAG                         ATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAAT
genomic: TTTTCCTCTTCTTCGGTGTGTTTACTTTGACAGTTGTGCAGGCTAGTCAGgtatgtctta ... catgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgatctgaagcacgtgccttttttttttttccctactactttcatgacacagATATCACGCAATATCACAACAAATGAAATGGCAAATGCACTGCGGTATAATTACCTCAGAGGTCCAGGTGGTAGATTCAGAAACCCATATGATCATGGTA
 ctttgat  putative branch site (score: 5)
               cgtgcctttttttttt  putative PPT
                     tttttttttttt  TA-rich tract