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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttctcaatttccttcagctttgtgcataatttgttctcatacatgaaatcttgagaataaataaggctttattatctttttaattaatctttttaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCGCGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT

Basic information

species Glycine max
transcript GLYMA20G28740.1
intron # 10
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


 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
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttctcaatttccttcagctttgtgcataatttgttctcatacatgaaatcttgagaataaataaggctttattatctttttaattaatctttttaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCGCGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT

- - - - - tccttca
- - - - - - - - - - - -tgcataa
- - - - - - - - - - - - - - - - - - - catacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - agaataaa