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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAATTTAATAAGGCTGCACAGTCTTTAACAGATGCTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAGgtagcttattgcaccaataattgcatgttactataataaatgactctcttattgaagtagttcttaccaagttttctttacattcttag

Basic information

species Glycine max
transcript GLYMA03G36550.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G36550.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os03g07080.1 (Oryza sativa), 5'ss of exon 6
GTTGAATTTAATAAGGCTGCACAGTCTTTAACAGATGCTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAGgtagcttattgcaccaataattgcatgttactataataaatgactctctta-ttgaagtagttct-taccaagttttctttacattcttag--
||||| |||||||||||||||||||||||||| |||||  | |||||| |  |||| |  |||   || || | | ||||| ||||||||            || ||    |  |   | | |  |      || | | |||   || |  | | | || | |||||        |    
GTTGAGTTTAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCAGCTGCTCAAAGAAAAGTGGCTTTAACTCGATTGATTAAGgtatgccccaaatttaaaaacaagaaatatgtcttacgacctgtgctgtcaattgttatattaatgtgctaattcttcttcttgactgtgcag

upper sequence: GLYMA03G36550.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os03g07080.3 (Oryza sativa), 5'ss of exon 6
GTTGAATTTAATAAGGCTGCACAGTCTTTAACAGATGCTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAGgtagcttattgcaccaataattgcatgttactataataaatgactctctta-ttgaagtagttct-taccaagttttctttacattcttag--
      |||||||||||||||||||||||||| |||||  | |||||| |  |||| |  |||   || || | | ||||| ||||||||            || ||    |  |   | | |  |      || | | |||   || |  | | | || | |||||        |    
------TTTAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCAGCTGCTCAAAGAAAAGTGGCTTTAACTCGATTGATTAAGgtatgccccaaatttaaaaacaagaaatatgtcttacgacctgtgctgtcaattgttatattaatgtgctaattcttcttcttgactgtgcag

upper sequence: GLYMA03G36550.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G118467_T03 (Zea mays), 5'ss of exon 6
GTTGAATTTAATAAGGCTGCACAGTCTTTAACAGATGCTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAGgtagcttattgcaccaataattgcatgttactataataaatgactctcttattgaagtagttcttaccaagtt--ttctttacattcttag-----
||||| || |||||||||||||||||||||||||||||| | |||||  |  | ||||| | |   || || | | ||||| |||| ||     |    |  ||  |||  || ||| |||         |  |  |||| | | | || | || | ||   || ||| ||||  |       
GTTGAGTTCAATAAGGCTGCACAGTCTTTAACAGATGCTATTATTCCTGCTGCCCAGAAAAGAGTGGCTTTAAGTCGATTGATTAAAgtgagaaaaacaatgaaagatt--atattattatgtccttcatcagttctatttatg-aattttaacaatgtcccttttttccatttcttttgaag

upper sequence: GLYMA03G36550.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G043509_T02 (Zea mays), 5'ss of exon 6
GTTGAATTTAATAAGGCTGCACAGTCTTTAACAGATGCTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAGgtagcttattgcaccaataattgcatgttac-tataataaatgactct-cttattgaagtagttcttaccaagttttctttacattcttag
||||| || ||||||||||||||||| |||||||||||  | |||||  |  ||||||| | |   || || ||| | ||| |||| |||    |    |  ||  |||  ||  ||  |    | | |   |||  ||||| |  |   |  |  |   ||  |  | | ||   ||
GTTGAGTTCAATAAGGCTGCACAGTCCTTAACAGATGCGATTATTCCTTCTGCTCAGAAAAGACTGGCTTTAAATCGTTTGATTAAAgtaagaaaaacaatgaaacattatattatatatcctgtcattagttctatttattaattttaataatgtccctttccccatccctttaaag

upper sequence: GLYMA03G36550.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G124051_T01 (Zea mays), 5'ss of exon 6
GTTGAATTTAATAAGGCTGCACAGTCTTTAACAGATGCTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAGgt--agct--tattgcaccaataattgcatgttactataataaatgactctcttattgaagtagttct-taccaagttttctttacattcttag
|| || || ||||||||||||||||||||||| |||||  | |||||  || |||| || ||    ||  | ||| | |||||||||||  | |   ||| | | | | || |  |   ||   |  || |||  ||  | |||    ||  ||| |  |||  | | | | |  |     
GTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCTGCCGCTCAAAAAAAGTTAGCTCTAAATCGTTTGGTTAAGgtgcaaccaatatgggaactacaaatataccataa-gtgctacatgg-tcgatcattaccttacatctattacaatctctatctgccatgcag-

upper sequence: GLYMA03G36550.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 5
GTTGAATTTAATAAGGCTGCACAGTCTTTAACAGATGCTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAGgtagctt-attgcacc--------aataattgcatgttactataataaatgactctcttattgaagtagttcttaccaagttttctttacattcttag
|||||||||||||||||||| |||||||| || || |||||| ||||||   |||| |||||||||||  | ||| || | |||||||| || | | ||||          || | |||| | ||         | |   | | || |||   |  |   |   ||  | |  ||  |||  |||
GTTGAATTTAATAAGGCTGCCCAGTCTTTGACGGACGCTGTGGTTCCAAGTGCTCAAAAGAAAACTGCTCTAAATCGACTAGTTAAGgtggcctgactgcatttgaagttaaacatttgctttttgtctcctagattttgttttttgttggcctcttaacttgaaatatctaattctatttgtag

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|7042673|gb|AW472567.1|AW472567
EST:     CTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAG                         GATAATGTTGCACTAATAGTTGTTTTAGAAGCAAAAGTTAACAATCAGCCT
genomic: CTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAGgtagcttatt ... acattcttagGATAATGTTGCACTAATAGTTGTTTTAGAAGCAAAAGTTAACAATCAGCCT
EST: gi|9204144|gb|BE330368.1|BE330368
EST:     CTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAG                         GATAATGTTGCACTAATAGTTGTTTTAGAAGCAAAAGTTAACAATCAGCCT
genomic: CTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAGgtagcttatt ... acattcttagGATAATGTTGCACTAATAGTTGTTTTAGAAGCAAAAGTTAACAATCAGCCT
EST: gi|151401049|gb|EV270863.1|EV270863
EST:     CTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAG                         GATAATGTTGCACTAATAGTTGTTTTAGAAGCAAA-GTTAACAATCAGCCT
genomic: CTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAGgtagcttatt ... acattcttagGATAATGTTGCACTAATAGTTGTTTTAGAAGCAAAAGTTAACAATCAGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAATTTAATAAGGCTGCACAGTCTTTAACAGATGCTGTGATTCCAACCACTCAGAAGAAAACTGCCTTGAATAGATTGGTTAAGgtagcttattgcaccaataattgcatgttactataataaatgactctcttattgaagtagttcttaccaagttttctttacattcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA