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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggttatgttgaagctttcagctgtaatgaacattttacaccaagttcgattaattagaagagagaatttggcacagaacgcatcctaacatttaatg...

Basic information

species Glycine max
transcript GLYMA20G24070.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24070.2 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 11
ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggttatgttgaagctttcagct--gtaatgaacattttac-accaagttcgattaattagaaga-----------gagaatttggcaca-gaacgcatcctaaca----tttaatg--------------------------------------
||||||| || |||||||||||||| || || || || || || || ||||||||||| |||||||||||| |||| ||||||||   || | ||      ||    |  |||   || |||||      |||    | |   |     |            | | | || |||| ||| | | | ||| |    ||  ||                                       
ATATTACACATCCAACTCCTGATCTTACGGGGTACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttcttttctgttcttttattgagtagcaaagattttcttggtaagagtaactggctgcttcatactccacctcaatattatgacacatgaatgtaacttaatagatcttctatattttttactctacctcaatattttcttgttactttcag

upper sequence: GLYMA20G24070.2 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G094497_T02 (Zea mays), 5'ss of exon 10
ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggtt---atgttgaagctttcagctgtaatgaacattttacaccaagttcgattaattagaagagagaatttggc--acagaacgcatcctaacatttaatg----------------------------------------------------------------------------------------
|||| || |||||||||||||| || || ||||| || |||||||| ||||||||||| || ||||||||  |||| |||||||||  ||   |||||     ||   |   ||   ||  ||  ||    |  | |   |  |     |     | |  |  |   |||   |  ||   |||                                                                                            
ATATCACACACCCAACTCCTGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttctatgttttctattcttgagttatcaaatgttacactttcacatggggcagctctggaattatttataactaatttaacattttttattttttttctcatattgatatagaatgtgaagtctttgtttatttttactaccttgatagcttatctgtgttgatgtgatggcattatattctttcag

upper sequence: GLYMA20G24070.2 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G181151_T03 (Zea mays), 5'ss of exon 11
ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggt-----tatgttgaagctttcagctgt--aatga-acatttt-----acaccaagttcg--attaattagaagagagaatttggcacagaacgcatcctaacatttaatg---------------------------------------------------------------------------------
|||| || ||||||||||| || || || ||||| || |||||||| ||||||||||| || ||||||||  |||| |||||||||  |     | | ||  |   || || | |  ||||  | |  ||      |  || ||  |  |||| ||| ||   |  |||| |||         | || | |||| ||                                                                                  
ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggtctggaattatttataactaa--atttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcag

upper sequence: GLYMA20G24070.2 (Glycine max), 5'ss of exon 12
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 5'ss of exon 10
ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggttatgttgaagctttcagctgtaatgaacattttacaccaagttcgattaattagaagagagaatttggcacagaacgcatcctaacatttaatg-----
||||||| ||||||| ||||||||| ||||||||||| || || || || || ||  | ||  ||||| |  | || ||||||||    | || | || |  | |  ||   | | || |        | || | ||  | |          ||| | |   |       ||    |||||||     
ATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgta---tgtgctcaatccctgaattgggtttatcagt--ggtgttattttgctttgtgatgttgtgtttttttgtatgtattaatcgcttttttttaatgttgat

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|120495604|gb|EH223771.1|EH223771
EST:     CGACAGGCAGCTGTATAATAGACAG                         ATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG
genomic: CGACAGGCAGCTGTATAATAGACAGgtgggttatg ... aactgggcagATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG
EST: gi|16276790|gb|BI942045.1|BI942045
EST:     ATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG                         ATATACCCACCAATCA
genomic: ATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggttatg ... aactgggcagATATACCCACCAATCA
EST: gi|21256304|gb|BQ453192.1|BQ453192
EST:     TATCACTGAGGGGCAGATATACATCTTACTGGCAGCTGTATAATAGACAG                         ATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG
genomic: TATCACTGAGGGGCAGATATACATC-GACAGGCAGCTGTATAATAGACAGgtgggttatg ... aactgggcagATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG
EST: gi|193476671|gb|FK439532.1|FK439532
EST:     ATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG                         ATATACCCACCAATCAACGTCCTCCCA
genomic: ATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggttatg ... aactgggcagATATACCCACCAATCAACGTCCTCCCA
EST: gi|16279439|gb|BI943437.1|BI943437
EST:     ATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG                         ATATACCCACCAATCAACGTCCTCCCATCACTATCTCAGTTGATGAAG
genomic: ATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggttatg ... aactgggcagATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG
EST: gi|16276744|gb|BI942021.1|BI942021
EST:     ATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG                         ATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG
genomic: ATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggttatg ... aactgggcagATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG
EST: gi|37996030|gb|CF807619.1|CF807619
EST:     TGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG                         ATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG
genomic: TGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggttatg ... aactgggcagATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG
EST: gi|16278548|gb|BI942962.1|BI942962
EST:     ATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG                         ATATACCCACCAATCAACGTGCTCCCATCACTATCTCGGTTGATGAAG
genomic: ATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggttatg ... aactgggcagATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG
EST: gi|21601974|gb|BQ612305.1|BQ612305
EST:     GGCAGCTGTATAATAGACAG                         ATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG
genomic: GGCAGCTGTATAATAGACAGgtgggttatg ... aactgggcagATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAG
EST: gi|19346883|gb|BM891771.1|BM891771
EST:     ATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG                         ATATACCCACCAATCAACGTCCTCCCA
genomic: ATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggttatg ... aactgggcagATATACCCACCAATCAACGTCCTCCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggttatgttgaagctttcagctgtaatgaacattttacaccaagttcgattaattagaagagagaatttggcacagaacgcatcctaacatttaatg

- - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG