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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAAGTGGGGGCATAATCAACATGATGGGGACCTATCAAATAGCATTGGTTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgtatatttgcatgcattcatccttttttgacgaattaggaatttatgttgtcttgtttgtgttactgtgcctgcag

Basic information

species Glycine max
transcript GLYMA03G42430.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G42430.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os12g31380.1 (Oryza sativa), 5'ss of exon 4
CGAAAGTGGGGGCATAATCAACATGATGGGGACCTATCAAATAGCATTGGTTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgtatatttgcatgcattcatcctttt-ttgacgaattaggaatttatgttgtcttgtttgtgttactgtgcctgcag---------------------------
 |||||||| || |||||||| |||||||| || ||||| |||||  | || |||||||||||||| ||||| |||||||| |||||||| || ||||||||| ||     ||| ||  || | || ||||   || ||   ||   |||||  || |||   ||||     |  |                            
TGAAAGTGGAGGAATAATCAATATGATGGGCACTTATCAGATAGCTCTCGTCGCTCACAGTATGAACAAACCTGTTTATGTGGCTGCTGAAAGTTACAAGgta-ataacattgcttttctcatattgttgatcgatgagctcttc-cgttgttatgcttgg--tactagaaatatataaggtggtacgcagaaaaaatctccta

upper sequence: GLYMA03G42430.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G084647_T01 (Zea mays), 5'ss of exon 4
CGAAAGTGGGGGCATAATCAACATGATGGGGACCTATCAAATAGCATTGGTTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgta-tatttgc-atgcattcatccttttttgacgaattagg--aatttatgttgtcttgttt----gtgttactgtgcctgcag----------------
 || || || || |||||||| |||||||| || ||||| |||||  | || ||||| | |||| | ||||| |||||||| || ||||| |||||||||||| |   ||  |||      | |||   | |   ||||      |||   |  |||| |||    |  | | |     || |                 
TGAGAGCGGAGGAATAATCAATATGATGGGCACTTATCAGATAGCTCTTGTGGCTCATACTATGGACAAACCTGTTTATGTGGCAGCTGAAAGCTACAAGgtaatgcatgttatgataatgtacttcaataatatattatccttgtttcactcatcttatttctttgcatcattacttttgtaatttaatgaatttggta

upper sequence: GLYMA03G42430.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G72340.1 (Arabidopsis thaliana), 5'ss of exon 4
CGAAAGTGGGGGCATAATCAACATGATGGGGACCTATCAAATAGCATTGGTTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgtatatttgcatgcattcatcc--ttttttgacgaattaggaatttatgttgtcttgtttgtgttactgtgcctgcag
 |||||||| || || |||||||||||||| || || ||||| ||| | || || ||||| ||||| ||||| || ||||| ||||||||||| ||||||||| |||   | |  || ||    |    |    |   ||   || ||| |  |    ||||||   ||         
AGAAAGTGGCGGTATTATCAACATGATGGGAACATACCAAATCGCACTTGTGGCACACAGCATGAACAAACCGGTCTATGTTGCTGCTGAGAGTTACAAGgta-attgaaacggttttataagatcccatagtaagagagtggttaatgata-caaagttgtgtatttgcag------

upper sequence: GLYMA03G42430.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G53880.1 (Arabidopsis thaliana), 5'ss of exon 6
CGAAAGTGGGGGCATAATCAACATGATGGGGACCTATCAAATAGCATTGGTTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgtatatttgcatgcattcatccttttt-------tgacgaattaggaatttatgttgtcttgtttgtgttactgtg--cctgcag------
 |||||||| || ||||| ||||||||||| || || ||||| ||  | || || || ||||||||||||||||| ||||| ||||| ||||| |||||||||   |  ||    || |    ||||       |||      |   ||  ||| |   |  | |   ||  |||   | ||||       
TGAAAGTGGCGGGATAATTAACATGATGGGAACTTACCAAATCGCCCTAGTCGCACAGAGTATGAATAAACCAGTCTATGTAGCTGCAGAGAGTTACAAGgtaacctcccaaaactttaaaagttttaaaaacttgattgcaaaaacatcaatgatccatcatcttctttcttgttttcttgcaagcgaag

upper sequence: GLYMA03G42430.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv09s0002g00390.t01 (Vitis vinifera), 5'ss of exon 7
CGAAAGTGGGGGCATAATCAACATGATGGGGACCTATCAAATAGCATTGGTTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgtatatttgcatgcatt-catccttttttgacgaattaggaatttatgttgtc--ttgtttgtgttactgtgcctgcag--------------------------
 |||||||| || ||||| |||||||||||||| |||||||| |||||||| |||||||| ||||| |||||||||||||| |||||||| ||||||||||||| ||   |   |   ||| | || |  |  | |  || |      |  ||   |  |  | |||||    ||  |                           
TGAAAGTGGAGGTATAATTAACATGATGGGGACATATCAAATCGCATTGGTGGCTCACAGCATGAACAAACCAGTTTATGTTGCTGCTGAAAGCTACAAGgtatgttgaaagaaaaaacataccttctgtaatagtctggtagaggaatcatcggctactgattttacttccacttgacaaatcatcacatactttgctttgcag

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|193644142|gb|FK592491.1|FK592491
EST:     TTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAG                         TTTGCTCGCCTTTACCCTCTTGACCAAAAGGATTTAGCCCCTGCGTTACGG
genomic: TTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgtatatttgc ... gtgcctgcagTTTGCTCGCCTTTACCCTCTTGACCAAAAGGATTTAGCCCCTGCATTACGC
EST: gi|254329055|gb|GR833427.1|GR833427
EST:     TTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAG                         TTTGCTCGCCTTTACCCTCTTGACCAAAAGGATTTAGCCCCTGCATTACGC
genomic: TTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgtatatttgc ... gtgcctgcagTTTGCTCGCCTTTACCCTCTTGACCAAAAGGATTTAGCCCCTGCATTACGC
EST: gi|8670487|gb|BE191594.1|BE191594
EST:     TTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAG                         TTTGCTCGCCTTTACCCTCTTGACCAAAAGGATTTAGCCCCTGCATTACGC
genomic: TTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgtatatttgc ... gtgcctgcagTTTGCTCGCCTTTACCCTCTTGACCAAAAGGATTTAGCCCCTGCATTACGC
EST: gi|31473972|gb|CD416000.1|CD416000
EST:     TTGCTCACAGTATGTATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAG                         TTTGCTCGCCTTTACCCTCTTGACCAAAAGGATTTAGCCCCTGCATTACGC
genomic: TTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgtatatttgc ... gtgcctgcagTTTGCTCGCCTTTACCCTCTTGACCAAAAGGATTTAGCCCCTGCATTACGC
EST: gi|22927216|gb|BU544355.1|BU544355
EST:     TTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAG                         TTTGCTCGCCTTTACCCTCTTGACCAAAAGGATTTAGCCCCTGCATTACGC
genomic: TTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgtatatttgc ... gtgcctgcagTTTGCTCGCCTTTACCCTCTTGACCAAAAGGATTTAGCCCCTGCATTACGC
EST: gi|7639253|gb|AW733580.1|AW733580
EST:     TTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAG                         TTTGCTCGCCTTTACCCTCTTGACCAAAAGGATTTAGCCCCTGCATTACGC
genomic: TTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgtatatttgc ... gtgcctgcagTTTGCTCGCCTTTACCCTCTTGACCAAAAGGATTTAGCCCCTGCATTACGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAAGTGGGGGCATAATCAACATGATGGGGACCTATCAAATAGCATTGGTTGCTCACAGTATGAATAAACCAGTTTATGTCGCTGCTGAGAGCTACAAGgtatatttgcatgcattcatccttttttgacgaattaggaatttatgttgtcttgtttgtgttactgtgcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT