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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagagctaggtccgaactaattcatgcaatttgaaaatctcattaaagtaaaccctacccccttcccaacagcaacctcatggaacaataaacaaaataaagaaaatgaaccagctattacctggatacacaaaatgattagtttgcaattccaacttttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATG

Basic information

species Glycine max
transcript GLYMA17G05410.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 11
gtatagagctaggtccgaactaattcatgcaatttgaaaatctcattaaagtaaaccctacccccttcccaacagcaacctcatggaacaataaacaaaataaagaaaatgaaccagctatta-cctggatacacaaaatgattagtttgcaattccaacttttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATG
                                   | | ||   ||| || ||     |  | |      || |  ||| ||    || | | |   |  | |           || || ||   || | ||    ||         | |  |||      ||| |  ||||||| | |||||| || ||||||||||| || ||  |||| || || |||||||| ||||||||||| || || ||||| ||||||||
-----------------------------------gtatataatattgaaatag-tggtctctcaaatgaaaaataaacttcgaaaaatattgaggcatgttatttgtcgatgtcatctgttggtcttgttatgtgaatcctaagactagttattatcttgtttct-cagTATCTTAACACAGCTGAATTTGCAATGCGCGAAGAGCTGTCCCTGAAGGCAGCTATCCTTGCTGAGAAATTCGCTCCAGATCTTTCATG

upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 12
gtatagagctaggtccgaactaattcatgcaatttgaaaatctcattaaagtaaaccctacccccttcccaacagcaacctcatggaacaataaacaaa--ataaagaaaatgaaccagctattacctg-gatacacaaaatgatta-gtttgcaattccaactttt---ttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATG
                                                                         | | ||    | ||               |||  | | || || |  | |||     |  |  |  | |   || |  || |    |  || ||   |   |||| ||    ||||| || |||||||||||||| || ||||| || || |||||||||||||| || || ||||                
-----------------------------------------------------------------------gtaactactcttttgaggggggggggggtcttaaccacactgtactattttttattcatgtcattcttactttctaagGCTGAATCCTCTTCTCTTACCTCACAGTACCTTGATACAGCAGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTG----------------

upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 11
gtatagagctaggtccgaactaattcatgcaatttgaaaatctcattaaagtaaaccctacccccttcccaacagcaacctcatggaacaataaacaaaataaagaa--aatgaaccagctattacctggatacacaaaatgattagtttgcaattccaacttttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATG-----------
                                                  ||||    | |    |        |         ||     ||| |  | || |  |    | |  ||  |  | ||||  | |    |||  | | |   |  |||  || |      |||| ||    ||||| || |||||||||||||| || ||||| || || |||||||||||||| || || ||||| ||| | || |  ||           
--------------------------------------------------gtaattaat-ctttgtgtgtgtgtgtggggggggggggtcttaaccgcactatactattgtttattcatgtcattcctgctttct---aatattgaatcctcttttcttacctc-----agTACCTTGATACAGCTGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCACAACTATTGTGGTAAGATTTTG

upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 12
gtatagagctaggtccgaactaattcatgcaatttgaaaatctcattaaagtaaaccctacccccttcccaacagcaacctcatggaacaataaacaaaataaagaaaatgaaccagctattacctggatacacaaaatgattagtttgcaattccaacttttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATG
                           |     ||  |  |  | ||| | |||    ||   | |       ||   ||| |||       ||    || | | |  | | |  |    ||   | | |    ||   | |||  | | |  |  || | | ||| ||||||| |||||||| |||||| | ||||| || ||||| ||||||||||| ||||| ||||||||||||||||| || || || |||||
--------------------------gtaagtctttgaccttactttatattaa----tatttcttgatttttagtctccttatgatttgtgaagtttaacagaaaggaaggattaa--gttgtgtag-tgtttaa---gcttacatggaagctaaaaatatattgcagTATCTTAGCACAGCAGAGTTTTCCATGCGGGAAGAATTATCACTTAAAGCTGCTATCCTTGCTGAGAAGTTTGCTCCTGATCTATCATG

upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatagagctaggtccgaactaattcatgcaatttgaaaatctcattaaagtaaaccctacccccttcccaacagcaacctcatggaacaataaacaaaataaagaaaatgaaccagctattacctggatacacaaaatgattagtttgcaattccaacttttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATG
                                                  ||||  | |   || | ||  |        |  || |    | |||| || |   |  || ||   | || |   |      |||       | |    |||    || |   ||| ||||||| |||||||| || ||| | ||||| |||||||| ||||||||||| ||||||||||||||||||||||| || || ||||||||
--------------------------------------------------gtaagtctttgaccttccctcatgat----ttgtgaagt--ttaacagaa-aggaaggattaagttggtagtgtttaagcttaca-------tggaacccaa----aaatacattgcagTATCTTAGCACAGCAGAATTTTCTATGCGGGAGGAATTATCACTTAAAGCTGCTATTCTTGCTGAGAAGTTTGCTCCTGATCTTTCATG

upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 11
gtatagagctag-gtccgaactaattcatgcaatttgaaaatctcattaaagtaaaccctacccccttcccaacagcaacctcatggaacaataaacaaaataaagaaaatgaaccagctattacctggatacacaaaatgattagtttgcaattccaacttttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATG
||| | |  ||  |   |||   | | |     ||| ||| ||||  | || |   |  ||  |  ||    |  |   |  || | ||          | || | |   |  | | | |   |     | |||    || || |      |  |    || ||||  ||||||||||||  || || ||||| ||||| |||||||||||||| |||||||| || || |||||||| ||||| || ||||| |||||
gtacacaaatattggaagaaaatagtaacttggtttaaaattctcgatcaaatcttctatattcaattttttaatgttgcaccaagaaa------gtgcagtagaaatttttcatctggtgcaaaacaaa-acaagggatcat-accactaacatatgtctgtttttcagTATCTCAGCAGTGCTGACTTTGCTATGCGCGAGGAATTGTCACTAAAAGCAGCAATCCTAGCTGAGAAATTTGCCCCTGACCTATCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagctattacctggatacacaaaatgattagtttgcaattccaacttttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATG
                                            cttttttgt  CT-rich tract
                    aaaatgattagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagagctaggtccgaactaattcatgcaatttgaaaatctcattaaagtaaaccctacccccttcccaacagcaacctcatggaacaataaacaaaataaagaaaatgaaccagctattacctggatacacaaaatgattagtttgcaattccaacttttttgtagTATCTCAGCACAGCGGAGTTTGCAATGCGTGAGGAATTGTCACTTAAAGCAGCTATTCTTGCTGAGAAGTTTGCACCAGACCTTTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT