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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttctcaatttccttcagctttgtgcataatttgttctcatacatgaaatcttgagaataaataaggctttattatctttttaattaatctttttaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCGCGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT

Basic information

species Glycine max
transcript GLYMA20G28740.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28740.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 5
----cttctcaatttccttcagctttgtgcataatttgttctcatacatgaaatcttgagaataaataaggctttat--tatctttttaattaatctttttaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCGCGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
           || |   |    ||| ||   ||  |||  | | || ||| |  |||    | | |   | |  ||  ||  |||||  ||||| |  |   |||||| |||||||| ||||||||||||||||| ||    || |||||| | ||   ||  ||  | || || |  | ||||   || ||||||||    || 
agggagaagggatctgtgttctatttctg-gcaaactgtctttacac-tgatacattgtc--tgatttctgttacatgataaatttttgcttaatttcatg--cagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTGTATCGGCTGTATGAACAACCAGAGTCATACGGAAACTGTTCTATCTACG

upper sequence: GLYMA20G28740.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G322090_T01 (Zea mays), 3'ss of exon 6
---cttctcaatttccttcagctttgtgcataatttgttctcatacatgaaatcttgagaataaataaggctttattatctttttaattaatctttttaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCGCGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
          || |     |  ||  ||   ||  | |  | | ||    |   |      |   |    | | || || |||||  ||||| |  |   |||||| |||||||| ||||||||||||||||| ||    || |||||| | ||   ||  ||    || || |  | |||| | || || |||||    || 
gggagaaaggatctgtagtatattcctg-gcaagctatctttacactgatagattgtctcgtttctgttacatgataatttttttgcttaatttcatg--cagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTGTATCGGCTGTCAGAACAACCAGAGTCATATGGAAACAGTTCTGTCTACA

upper sequence: GLYMA20G28740.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 4
cttctcaatttccttcagctttgtgcataatttgttctcatacatgaaatcttgagaataaataaggctttattatctttttaattaatctttttaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCGCGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
        |   || ||   ||   |||  |||| |||    |       ||| | || || |  ||  || | |   || | ||   | | |    |||||| ||||| |||||||||||||||||||| |||||||| || ||| ||||    || ||||||||||||||||| ||||  ||   ||| ||    |||
-------gtaagctccaaagttccacatt-tttgatctttggc------ccttcaaaa-aagtttggtgttttgagtcttctgatgtttgtgtggtgcagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT

upper sequence: GLYMA20G28740.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 5
-cttctcaatttccttcagctttgtgcataatttgttctcataca---tgaaatcttgagaataaataaggc--tttattatctttttaattaatctttttac--cagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCGCGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
        ||  ||   ||| |   |  |||||  | |   | ||   | |||   |||       | | |   || |  ||  ||| | |   | || || |  |||||| ||||| |||||||||||||| || || |||||||| || ||| ||||    ||||||||||| |||||||| ||||  || |||||| |    || 
gtaagctcataccccctagcatctcgt-taattcctacctgttcaaaataaaaaactgaattgccttgaagtagttaaccattgtttgactcccttttctttctgcagTTACTGTGAATGCTTTGCTGCTGGGGTTTATTGCATAGAGCCATGTTCATGTATAGATTGCTTCAACAAACCTATCCATGAAGAAACTGTTTTGGCTACC

upper sequence: GLYMA20G28740.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
cttctcaatttccttcagctttgtgcataatttgttctcatacatgaaatcttgagaataaataaggctttattatctttttaattaatctttttac--cagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCGCGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
  |||     || || ||    | ||| |      |   | |  |    | ||         |  |   |||| || |      |||| ||| ||    |||||| ||||| |||||||||||||| ||||||||  |||| || ||| ||||||  || ||||| || |||||||||||||  || |||||||||  ||||
tgtctttgaatctttgagg--ggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT

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|192297452|gb|FG989861.1|FG989861
EST:     GGGGAGTCTTGCAAGCGTTGTAATTGTAAGAAATCAAAATGTTTGAAGCT                         TTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATG
genomic: GGGGAGTCTTGCAAGCGTTGTAATTGTAAGAAATCAAAATGTTTGAAGCTgtaagtttaa ... tttttaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATG
EST: gi|18730189|gb|BM525736.1|BM525736
EST:     GGGGAGTCTTGCAAGCGTTGTAATTGTAAGAAATCAAAATGTTTGAAGCT                         TTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATG
genomic: GGGGAGTCTTGCAAGCGTTGTAATTGTAAGAAATCAAAATGTTTGAAGCTgtaagtttaa ... tttttaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatcttgagaataaataaggctttattatctttttaattaatctttttaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCGCGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT
                                     aattaat  putative branch site (score: 3)
                                           tctttttacc  CT-rich tract
           aataaataaggcttta  TA-rich tract