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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGCGTGCCACTGCATTTGGTTTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgcaagcccatataagatgtattatatgttgttatttatctggaaattattacctgaacaattgcttaaaaatgccacttttcttttctag

Basic information

species Glycine max
transcript GLYMA14G01290.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 3
AGCGCGTGCCACTGCATTTGGTTTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgcaagcc-catataagatgt----attatatgttgttatttatctggaaattattacctgaacaattgcttaaaaatgccacttttcttttctag
||  ||||| || ||||||||  | |||||||||||||| || ||| | || ||||||||||| |||||||||||||||||  |||||||| | |||| || ||        | |   ||    |  |||||        | | | |||      |  | |   ||||  |  |  |     |||  | ||  ||
AGAACGTGCTACAGCATTTGGCCTTATGAAGATTGATGATGAAGGGAGGATCATTGAATTTGCAGAAAAGCCAAAAGGAGAGAAGTTGAAATCAATGATGgtaattgatgagtcatccgttgagaccatatgcaacctgatctgttgaagcatacatttcagtgattgtctgcatgt-----tttgatcttgcag

upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os08g25734.2 (Oryza sativa), 5'ss of exon 3
AGCGCGTGCCACTGCATTTGGTTTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgcaagcccatataagatgtattatatg-----ttgttattta----tctgga-----aattattac-ctgaacaattgcttaaaaatgccacttttcttttctag-------------
    ||||| |||||||| ||  | ||||| ||||| || || ||| | ||| |||||||||| || || |||||||||||||| |||||||| |||| || | ||  | || |  ||  ||   ||     |||| || ||    | ||       | ||||||| |   | | || | ||  ||  |   |||| ||  |||              
GAAACGTGCAACTGCATTCGGCCTCATGAAAATTGACGAGGAAGGGAGAATAGTTGAATTTGCAGAGAAACCAAAAGGAGAACAATTGAAAGCAATGATGgtatgc--aaatgacgtgcctttcttgctaacttgtgatatacagttgtgagatatcagttattacaccacatacttccatatcaaaactcattttgttgcctattttcgtcttgtag

upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G068506_T03 (Zea mays), 5'ss of exon 3
AGCGCGTGCCACTGCATTTGGTTTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgcaagccca-tataagatgtatta----tatgttgttatttatctggaaattattacctgaacaattgcttaaaaatgccacttttcttttctag-------
    ||||| |||||||||||  | ||||| ||||||||||| ||| | || ||||| |||||||| || || |||||||| ||||||||||| |||| || |  |  | |||    |   ||     ||  ||| | |  || ||   |  || |  |    ||   ||  || || ||| ||| ||  | | |       
GAAACGTGCAACTGCATTTGGCCTCATGAAAATTGATGAAGAAGGGAGGATCATTGAGTTTGCTGAGAAACCGAAAGGAGAGCAGTTGAAAGCAATGATGgtacacataatatgctttcctttcaagctaacttgatttacatttgtggacaatcattttgtaaac--ctacaatattccattttactcctttggattgtag

upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G163437_T01 (Zea mays), 5'ss of exon 3
AGCGCGTGCCACTGCATTTGGTTTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgcaagcccatataagatgtattatatgttgttatttatctggaaattattacctgaacaattgcttaaaaatgcca--cttttcttttctag-------------------------------------
    ||||| || ||||||||  | ||||| ||||| ||||| ||| | || ||||| |||||||| || || |||||||| ||||||||||| |||| || |    || ||||  ||  || | | |    |  || || || ||   |   |  |||||   |||   |  | |   | |||   | ||                                      
GAAACGTGCAACCGCATTTGGCCTCATGAAAATTGACGAAGAAGGGAGGATTATTGAGTTTGCTGAGAAACCGAAAGGAGATCAGTTGAAAGCAATGATGgta----cacataatttgccttttctttca--agctaacttgacatacatttgttgacaatcatttagtgaacctaaaatattcccctttaaaatgccttcatctcatatttctgtctgattgatgtag

upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 3
AGCGCGTGCCACTGCATTTGGTTTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgcaagcccatataagatgtattatatgttgttatt-tatctggaaattatta------cctgaacaattgc---ttaaaaatgccacttttcttttctag---------
|   ||||| |||||||||||| | ||||| |||||||| || ||| | ||| |||| || || ||||| |||||||||||  || ||| | | |||| || |      |   | |  | ||     | ||| || | |||    ||| |||      | |   | |||||   ||   | |     ||| ||| | |           
ACAACGTGCAACTGCATTTGGTCTTATGAAAATTGATGATGAAGGGAGGATAGTTGAGTTCGCAGAAAAACCAAAAGGAGAGAAGCTGAGATCAATGATGgtacaaatgtgataaactttttgaccctagttcttatgtctcctgattgttagagctccttttgcgattgcattttttcagttaagttttgcttgttttaccttttcag

upper sequence: GLYMA14G01290.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 3
AGCGCGTGCCACTGCATTTGGTTTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgcaagcc-catataagat--------gtatta---tatgttgttattta-------tctggaaattattacctgaacaattgcttaaaaatgccact----tttcttttctag---------------
|   || ||||||||||||||| | |||||||||||||| || || ||||||||||||||||| || || ||||||||||| || |||||||||||||||| |      || | | ||        ||||||   |||| | || | |        |||  || ||  ||  |  | | ||| |||| || ||   |    |||| |||||                 
AAAACGAGCCACTGCATTTGGTCTAATGAAGATTGATGAGGAAGGCCGTATAATTGAATTTGCAGAGAAACCAAAAGGAGAGCAATTGAAAGCTATGAAGgtagatgatatttgaaataaacattcgtattaatttatgcttttgtgttcctctattctacaattttgtagttttaaagttggttaagaaggctgatacgttttcctttctgaactgttccttttaag

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|9205235|gb|BE331459.1|BE331459
EST:     TAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAG                         GTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAAGAAATGCCT
genomic: TAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgcaagcccat ... tcttttctagGTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAAGAAATGCCT
EST: gi|13478311|gb|BG507837.1|BG507837
EST:     TAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAG                         GTTGATACTACAATTTTGGGT
genomic: TAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgcaagcccat ... tcttttctagGTTGATACTACAATTTTGGGT
EST: gi|22521682|gb|BU080493.1|BU080493
EST:     TAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAG                         GTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAAGAAATGCCT
genomic: TAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgcaagcccat ... tcttttctagGTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAAGAAATGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGCGTGCCACTGCATTTGGTTTGATGAAGATTGATGAAGAGGGGCGTATAATTGAATTTGCTGAAAAGCCAAAAGGAGAACAGTTGAAAGCTATGAAGgcaagcccatataagatgtattatatgttgttatttatctggaaattattacctgaacaattgcttaaaaatgccacttttcttttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA