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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgtaaaccatggaaaatgctctatttttggccatttaaatatgtcaatgccattgcagatatgtagatgatgcttggaccaagttacttgcctgcttgaat...

Basic information

species Glycine max
transcript GLYMA14G37090.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G37090.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 10
GAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgtaaaccatggaaaatgctctatttttggccatttaaatatgtcaatgccattg-cagatatgtagatgatgcttggaccaagttacttgcctgcttgaat
||| || | ||| |||||||| |||||||||||||||| ||||||||| || || || ||||| || ||||||||  | || || ||||||||||| |||||     | | ||    || |   |    |  |||||  |  |    | | | | |  | || |   || || |         ||     || |       
GAAGGGTAATGAAAAGGCTGTTGTTGCACGGCATGAAGTTGGTCATGCCGTTGTGGGAACTGCTGTAGCAAACCTATTGCCAGGGCAGCCACGTGTGGAGgtttga-acgcaagcaactatcgatagaacagtttaagaaaatgttcgtcttgggcttacattttagtgttgttctt------ttttccaccag-------

upper sequence: GLYMA14G37090.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 9
GAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGg--taaaccatggaaaatgctctatttttggccatttaaatatgtcaatgccattgcagatatgtagatgatgcttggaccaagttacttgcctgcttgaat
||| || | ||| |||||||| ||||||||||||||||  ||||||||  | || || ||||| || || |||||||||||||||||||||||||||||||  | |||    | || | ||     |    | || | |        |||  |||  |  ||  |     ||||| | |   |                   
GAAGGGTAATGAAAAGGCTGTCGTTGCACGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCGAACCTTCTTCCTGGACAGCCACGTGTTGAGgtttgaacttaagcaattactga---tagaacaatctgagagaa--gatgtaatttgacttactttttcaatgct-gaatttaacag---------------

upper sequence: GLYMA14G37090.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G072865_T01 (Zea mays), 5'ss of exon 10
GAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgt--aaaccatggaaaatgctctatttttggccatttaaatatgtcaatgccattgcagatatgtagatgatgcttggaccaagttacttgcctgcttgaat
||| || | ||| || ||||| ||||| ||||||||||  ||||||||  | || || ||||| || |||||||| |||||||||||||||||||| |||||   |||    | || | ||      | |  || |   |||    |    |      |   | |  ||| ||  |  | ||                    
GAAGGGTAATGAAAAAGCTGTTGTTGCGCGGCATGAAGTAGGTCATGCACTCGTGGGAACTGCTGTAGCAAACCTCCTTCCTGGACAGCCACGTGTGGAGgtttgaacttaagcaattactga----tagaacaatctgataaaaaaggatctaatttggctttttaatgttgaatttaacag-------------------

upper sequence: GLYMA14G37090.1 (Glycine max), 5'ss of exon 11
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 5'ss of exon 10
GAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgtaaaccatggaaaatgctctatttttggcca-------tttaaatatgtcaatgccattgcagatatgtagatgatgcttggaccaagttacttgcctgcttgaat
 ||||| |||||||| ||||| |||||| ||||||||||||| |||||||| || ||||| || |||||||  |||||| |||||||| | |||||||||||||| ||  || ||     | ||  | |  |       |||| || ||| |||||   |||  |||  ||    ||  || |                        
AAAAGGTAGTGAGAAAGCTGTGGTTGCAAGGCATGAAGCTGGGCATGCTGTTGTTGGTACAGCTGTTGCAAGTCTTCTTTCTGGACAGTCCCGTGTTGAGgtaaagcagtgagaaccgcatgttgcttgatactcattttttacatgtgttaatgct-ctgctaatacatattgtatttttag------------------------

upper sequence: GLYMA14G37090.1 (Glycine max), 5'ss of exon 11
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 5'ss of exon 10
GAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgtaaaccatggaaaatgctctatttttggccatttaaatatgtcaatgccattgcagatatgtagatgat----gcttggaccaagttacttgcctgcttgaat
 ||||| | ||||||||| || || ||| ||||||||||||| ||||| ||||| ||||| || |||||||| |||||| |||||||||||||||||||||||||  ||| ||||  || | | |      |     || |||  |||   ||    |  || | |||||    | || |  ||  ||  | |  |  |     
AAAAGGCAATGAGAAGGCAGTGGTCGCAAGGCATGAAGCTGGGCATGCAGTGGTTGGTACCGCTGTTGCAAATCTTCTTACTGGACAGCCACGTGTTGAGgtaaa--atgcaaaa-actttgtctacatttacgctcat-tgtttatgttgtttagtacgtgcaaatgattcaagttttgctcatctttgtggtgttgtcag--

upper sequence: GLYMA14G37090.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 5'ss of exon 10
GAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgtaaaccatggaaaatgctctatttttggccatttaaatatgtcaat--gccattgcagatatgtagatgatgcttggaccaagttacttgcctgcttgaat
| | ||||||||||||||||| |||||||||||||||||||||||||| || || || ||||| ||||| || |||||||||||||||||||||||||||||||   ||    |      |     |    ||||   | |     |   | | |    |  | |  |   | | ||||  |  |      |  |   ||  
GCAGGGAAGTGAGAAGGCTGTTGTTGCACGGCATGAAGCTGGTCATGCAGTAGTGGGAACTGCTGTTGCTAATCTTCTTCCTGGACAGCCACGTGTTGAGgtaagttattaggaccttatttacaataaatattttcctttactgcttaacaagtttcaaattatttaacctccctggagaatttggaagacacgtgaga--

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|17400703|gb|BM177485.1|BM177485
EST:     TGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAG                         AAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACT
genomic: TGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgtaaaccatg ... atgttatcagAAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACT
EST: gi|192302740|gb|FG993760.1|FG993760
EST:     TGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAG                         AAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACT
genomic: TGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgtaaaccatg ... atgttatcagAAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACT
EST: gi|213606222|gb|DB961338.1|DB961338
EST:     TAGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAG                         AAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACT
genomic: TGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgtaaaccatg ... atgttatcagAAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACT
EST: gi|20498713|gb|BQ273643.1|BQ273643
EST:     TGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAG                         AAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACT
genomic: TGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgtaaaccatg ... atgttatcagAAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGGAAGTGAGAAGGCTGTAGTTGCACGGCATGAAGCTGGTCATGCTGTGGTAGGTACTGCAGTTGCAAACCTTCTTCCTGGACAGCCACGTGTTGAGgtaaaccatggaaaatgctctatttttggccatttaaatatgtcaatgccattgcagatatgtagatgatgcttggaccaagttacttgcctgcttgaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG