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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtataatccaggccttaaatcgttttgtaaaatcaatgattatgggtgtgtgcacatatgtgtgtgcaatatttgaaattattagctattaagaatacggcctcccattccttttaattcaagttctttggtaaaaatgtagATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGCAGCCAAAGTGAGAGCTGGAAGTTACAGCGGAGGAATGAAACGCCGTCTCAGTGTTGCAA

Basic information

species Glycine max
transcript GLYMA06G20360.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G20360.2 (Glycine max), 3'ss of exon 11
lower sequence: AT3G47730.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatgtataatccaggccttaaatcgttttgtaaaatcaatgattatgggtgtgtgcacatatgtgtgtgcaatatttga--aattattagctattaagaatacggcctcccattccttttaattcaagttctttggtaaaaatgtagATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGCAGCCAAAGTGAGAGCTGGAAGTTACAGCGGAGGAATGAAACGCCGTCTCAGTGTTGCAA
                                       |||        || ||  | ||  ||  ||    || | |     ||| |    || ||||||||     | ||||  |        | |||  ||  |    || |||||     |||  ||| | || ||||||| ||| || || ||||  ||| | || || ||||||||||| |||||||||||||| || |||||||||||| 
-------------------------------------gtatgtacccaaatg-gtagaaatgagtcggttggttagtcggttggttacttcaaatcaagaatacttttcctcatttgtcgcttaaaatgttactttctcgtcatatagATGGTTGAGAAGTCACTGGCGGAGGTAAAACTAACAGAAGCAGGGAAAATCAGGGCAGGAAGTTACAGTGGAGGAATGAAACGGCGACTCAGTGTTGCAG

upper sequence: GLYMA06G20360.2 (Glycine max), 3'ss of exon 11
lower sequence: AT5G61730.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatgtataatccaggccttaaatcgttttgtaaaatcaatgattatgggtgtgtgcacatatgtgtgtgcaatat--ttgaaattattagctattaagaatacggcctcccattccttttaattcaa-gttctttggtaaaaatgtagATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGCAGCCAAAGTGAGAGCTGGAAGTTACAGCGGAGGAATGAAACGCCGTCTCAGTGTTGCAA
                                                 ||   |   | ||      |  |||||  || | |||  |   | |||  ||||     |   |   |||||   | |   | | ||     | || |||||| |  |||  | | | | ||| || |  || || |   | || ||| | ||||| ||||||||||| || ||||||||||| || || ||||||||||
-------------------------------------------------gtacatcaccctaataacataaaatatacttcatattcatgtgtgttacaaatatctgatttaa--acttttggctaagcatacctttacgtatatatagATTGCAGAGAAGTTACTGGTAGATGTGAAGCTAACAGGATCGGCGAAAATTAGAGCAGGAAGTTACAGTGGTGGAATGAAACGTCGGCTGAGTGTTGCAA

upper sequence: GLYMA06G20360.2 (Glycine max), 3'ss of exon 11
lower sequence: AT5G61690.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgtataatccaggccttaaatcgttttgtaaaatcaatgattatgggtgtgtgcacatatgtgtgtgcaatatttgaaattattagctattaagaatacggcctcccattccttttaattcaagttctttggtaaaaatgtagATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGCAGCCAAAGTGAGAGCTGGAAGTTACAGCGGAGGAATGAAACGCCGTCTCAGTGTTGCAA
                                            || |         | || |    ||||||          |  |   | |   |||     |   |||| |   |||  | |     || | |     | |||| | |  |||  | | | || || |||| ||| || |  || || ||||| ||||| ||||||||||| || ||||||||||| || |||||||||||  
-------------------------------------------gtaggccgactgaaaaatctcaaagtgcaaag---aggtctgatgattttattgaactttccaatccatgcaacttatcttacaagtttcgtttctgttatagACTGCTGAGAAGTTACTGGCGGATGTAAAACTGACAGGAGCGGCGAAAGTTAGAGCAGGAAGTTACAGTGGTGGAATGAAACGTCGACTCAGTGTTGCGG

upper sequence: GLYMA06G20360.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv17s0000g05850.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------gtatgtataatccaggccttaaatcgttttgtaaaatcaat--------gattatgggtgtgtgcac--atatgtgtgtgcaat--atttgaaattattagctattaagaatacggc---ctcccattccttttaatt----caagttctttggtaaaaatgtagATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGCAGCCAAAGTGAGAGCTGGAAGTTACAGCGGAGGAATGAAACGCCGTCTCAGTGTTGCAA
                               |     || |  |    |   ||   || | | | |   |         |||||  || | | |||  ||||   ||| || |  |||    || |     | | |  |  | | |   || | |||| | ||   |    ||| | |||         || || || | || |  ||||| |||||||| | ||||||  | ||||||||| |||||||||| ||||| || ||||||||||||||||| || |||||||| |
gtatgtactgagcaaaccccaataaggggccttcacctacttgatttttcctatttattggaagacttggtttttgtccaattattagtttttacaccaatatagatgttcacttcattcttgatgaactcgtgtcagtagaatgtctctcttctattcatatttcctggaacaaatgcttctacttttgtgcagGTTGCTCAAAAATCATTGGCAGAGGTGAAACTCACCCAAGCAGCCAAAATGAGAGCTGGGAGTTATAGTGGAGGAATGAAACGCCGCCTTAGTGTTGCTA

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|15662847|gb|BI700218.1|BI700218
EST:     TCCAACTCTTTGCTACTATTANAGGCCTGTCCCCAGCTTCCATAAAATCA                         ATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGCAGCCAAAGTG
genomic: TCCAACTCTTTGCTACTATTAAAGGCCTGTCCCCAGCTTCCATAAAATCAgtatgtataa ... aaaaatgtagATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGCAGCCAAAGTG
EST: gi|193669758|gb|FK612358.1|FK612358
EST:     TCCAACTCTTTGCTACTATTAAAGGCCTGTCCCCAGCTTCCATAAAATCA                         ATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGCAGCCAAAGTG
genomic: TCCAACTCTTTGCTACTATTAAAGGCCTGTCCCCAGCTTCCATAAAATCAgtatgtataa ... aaaaatgtagATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGCAGCCAAAGTG
EST: gi|193518779|gb|FK472752.1|FK472752
EST:     TCCAACTCTTTGCTACTATTAAAGGCCTGTCCCCAGCTTCCATAAAATCA                         ATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGC
genomic: TCCAACTCTTTGCTACTATTAAAGGCCTGTCCCCAGCTTCCATAAAATCAgtatgtataa ... aaaaatgtagATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGC
EST: gi|193661639|gb|FK602593.1|FK602593
EST:     TCCAACTCTTTGCTACTATTAAAGGCCTGTCCCCAGCTTCCATAAAATCA                         ATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGC
genomic: TCCAACTCTTTGCTACTATTAAAGGCCTGTCCCCAGCTTCCATAAAATCAgtatgtataa ... aaaaatgtagATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaagaatacggcctcccattccttttaattcaagttctttggtaaaaatgtagATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGCAGCCAAAGTGAGAGCTGGAAGTTACAGCGGAGGAATGAAACGCCGTCTCAGTGTTGCAA
                        ttttaat  putative branch site (score: 3)
                        ttttaattcaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtataatccaggccttaaatcgttttgtaaaatcaatgattatgggtgtgtgcacatatgtgtgtgcaatatttgaaattattagctattaagaatacggcctcccattccttttaattcaagttctttggtaaaaatgtagATTACCCAGACTTCATTAGCAGAGGTAAGACTCACGGATGCAGCCAAAGTGAGAGCTGGAAGTTACAGCGGAGGAATGAAACGCCGTCTCAGTGTTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA