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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataacttaaaagcatgtgctatgaaatagtttagaacagattttaacttgtaatacttttgctgattaatatagcttttaataacttcttgtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAGGTGGCCTTAGTTCACAAGGAAGCAGAGGAGAAGAGGGCAATGATTGAAG

Basic information

species Glycine max
transcript GLYMA18G46470.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46470.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g45070.1 (Oryza sativa), 3'ss of exon 4
ataacttaaaagcatgtgctatgaa-atagtttagaacagattttaacttgtaatacttttgctg---attaatatagcttttaataacttcttgtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAGGTGGCCTTAGTTCACAAGGAAGCAGAGGAGAAGAGGGCAATGATTGAAG
 ||     ||||| ||| |  | |  ||||      |||  |  || ||||||  |  | ||       || |  ||     || |   ||          ||||| |||||||| || ||||| || |||||||  || || ||||||||||| || ||  | || ||||||||||| ||||||||||| |||||| | || |
-tatagggaaagc-tgtaccttaactataggactacacatgtcata-cttgtatcatgtatggcatcctttgaactaaagccta-tgcatttgcaccctttcagGAGCAACTGGAAAAGAAGAAGGCTGAATATGCAGAGAAGATGAAGAACAAAGTCGCGATCGTCCACAAGGAAGCTGAGGAGAAGAGAGCAATGGTCGAGG

upper sequence: GLYMA18G46470.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G116538_T02 (Zea mays), 3'ss of exon 4
-------ataacttaaaagcatgtgctatgaaatagtttagaacagattttaacttgtaatacttttgctgattaatatagcttttaataacttcttgtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAGGTGGCCTTAGTTCACAAGGAAGCAGAGGAGAAGAGGGCAATGATTGAAG
       |   |  ||||| ||       | |  | |      |      |||   || |||   |     || | ||| |||  || ||| || ||   ||  |||||||||||||| || |||||||| ||||||| ||| || ||||| |||||||| ||  |  | |||| |||||| || |||||| | || ||| | || |
atggaggacgccgcaaaaggatagatccagtagaactaatatgccacccctaaaaggtgatatcatc----ataactat-gctcata-taatttatt-catgttcagGAACAACTGGAAAAGAAGAAAGCTGAATATGCTGAGAAGATGAAAAACAAGGTTGCAATGATCCACAGGGAAGCCGAAGAGAAGCGAGCGATGGTGGAGG

upper sequence: GLYMA18G46470.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g03180.t01 (Vitis vinifera), 3'ss of exon 4
-ataacttaaaagcatgtgctatgaaatagtttagaacagattttaacttgtaatacttttgctgattaatatagc-ttttaataacttcttgtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAGGTGGCCTTAGTTCACAAGGAAGCAGAGGAGAAGAGGGCAATGATTGAAG
 | ||   ||| | |  | | |   |  ||   |  ||  |||||   | ||  ||  | || || || | || |   | ||| ||||||  |  ||| |||||| || ||||||| ||||| ||||||||||  || |||||||| ||||| || || ||  |||||||| ||||||| || |||| ||||||||||||||
gagaagcaaaatgaactttcaaattaggagaacaatacgaattttgtttggtttta--tatgatgttttacattgaactctaacaacttcaagcatgatcagGAAGAATTGGAGAAGAAGAAGGCAGAATATGCAGAGAAAATGAAAAACAAAGTAGCATTGATTCACAAGCAAGCAGAAGAAAAGAAGGCAATGATTGAAG

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|192310351|gb|FK002231.1|FK002231
EST:     GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAG                         GAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
genomic: GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAGgtaatactta ... gtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
EST: gi|15337035|gb|BI497691.1|BI497691
EST:     GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAG                         GAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
genomic: GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAGgtaatactta ... gtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
EST: gi|9259721|gb|BE347868.1|BE347868
EST:     GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAG                         GAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
genomic: GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAGgtaatactta ... gtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
EST: gi|4296039|gb|AI442418.1|AI442418
EST:     GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAG                         GAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
genomic: GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAGgtaatactta ... gtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
EST: gi|298192129|gb|HO036211.1|HO036211
EST:     GGGAAAACAGCAAAAAGGCAGCTCCTGAAGCTGAGCTTAAAAAATTGGAG                         GAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
genomic: GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAGgtaatactta ... gtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
EST: gi|151394356|gb|EV264227.1|EV264227
EST:     GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAG                         GAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
genomic: GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAGgtaatactta ... gtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
EST: gi|12689896|gb|BG156232.1|BG156232
EST:     GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAG                         GAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
genomic: GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAGgtaatactta ... gtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
EST: gi|58022686|gb|CX709427.1|CX709427
EST:     GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAG                         GAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
genomic: GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAGgtaatactta ... gtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
EST: gi|192307960|gb|FG998963.1|FG998963
EST:     GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAG                         GAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
genomic: GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAGgtaatactta ... gtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
EST: gi|58019637|gb|CX706379.1|CX706379
EST:     GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAG                         GAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
genomic: GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAGgtaatactta ... gtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
EST: gi|192310350|gb|FK002230.1|FK002230
EST:     GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAG                         GAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG
genomic: GGGAAAACAGCAAAAAGGCAGCTCTTGAAGCTGAGCTTAAAAAATTGGAGgtaatactta ... gtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgtaatacttttgctgattaatatagcttttaataacttcttgtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAGGTGGCCTTAGTTCACAAGGAAGCAGAGGAGAAGAGGGCAATGATTGAAG
                                 taataac  putative branch site (score: 1)
                                       cttcttgt  CT-rich tract
                   attaatatagctttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataacttaaaagcatgtgctatgaaatagtttagaacagattttaacttgtaatacttttgctgattaatatagcttttaataacttcttgtgtgagcagGAACAACTGGAGAAAAAGAAAGCAGAATATGGTGAAAAAATGAAGAACAAGGTGGCCTTAGTTCACAAGGAAGCAGAGGAGAAGAGGGCAATGATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - catgtgc