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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaattatgatgctgtattggataaaaataattaagacatacagagattttgtttttatatcttatatgtggtcctaaaattatattgattcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCTGGTTTTGCACCCTATGAAAAGCGTATAACTGAGTTGCTGAAGGTTGGGA

Basic information

species Glycine max
transcript GLYMA10G37840.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G37840.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g38520.2 (Oryza sativa), 3'ss of exon 2
ttaaattat--gatgctgtattggataaaaataattaagacatacagagattttgtttttatatcttatatg-tggtcctaaaattatattgattcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCTGGTTTTGCACCCTATGAAAAGCGTATAACTGAGTTGCTGAAGGTTGGGA
|| ||| ||  ||| |||  ||  || |      ||      ||| |    ||  ||  |||  | | |    |   | |      || || |||     |||||| | | ||||||||||  |||||| |||||| | || || ||||||||||| ||||| |||||||| |||||||| |||||| | || || ||||| |
ttcaatgatttgatcctgctttatattatctgctttgcagtttactggccattatttcctattgcatttgcacttaccttgttggcatgttaatttg---cagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCTGGATTTGCTCCCTATGAGAAGCGTATCACTGAGCTTCTCAAAGTTGGCA

upper sequence: GLYMA10G37840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G850966_T03 (Zea mays), 3'ss of exon 2
ttaaattatgatgctgtattggataaaaataattaagacatacagagattttgtttttatatcttatatgtggtcctaaaattatattgattcaaaa--cagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCTGGTTTTGCACCCTATGAAAAGCGTATAACTGAGTTGCTGAAGGTTGGGA
 |  |  |||    ||  | | | ||  ||     |||  |||| |   ||||   ||   | || | ||||  | | |    |  ||  ||       |||||| |||  |||||||||    | || |||  ||| || |||||||||||||| ||||| || ||||| |||||||| |||||| | ||||||||||| |
ctgtac-atgtaaatgattagcacaagtatgcggtagatttacatat-ctttgcacttgattgttttctgtgtccttcattccaagttattttgttgttcagAAATCAACGAAGAGGGTGTCTATGGTCAGGGGCCTGATCAGAGAGGTTGCTGGGTTTGCTCCTTATGAGAAGCGTATCACTGAGCTTCTGAAGGTTGGCA

upper sequence: GLYMA10G37840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G850966_T01 (Zea mays), 3'ss of exon 3
ttaaattatgatgctgtattggataaaaataattaagacatacagagatt-ttgtttttatatcttatatgtggtcctaaaattatattgattcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCTGGTTTTGCACCCTATGAAAAGCGTATAACTGAGTTGCTGAAGGTTGGGA
                                    ||   | |||| ||  ||  |||    |||||  |  |       || |    | |||  ||  |    |||| |  || |||| ||      | | | |  |||||||       |   |  ||      | ||||   |  |  |||  | ||  ||      
---------------------------------cctgat-cagagaggttgctgggtttgctccttatgagaagcgt----atcactgAGCTTCTGAA-GGTTGGCAAGGACAAGCGTGCCCT------GAAGCTTGCTAAGAGAAAGCTTGGAACTCACAAGAGG-GCAAAGAAGAAGAGAGAGGAGATGGCGGG-----

upper sequence: GLYMA10G37840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G009936_T01 (Zea mays), 3'ss of exon 2
ttaaattatgatgctgtattggataaaaataattaagacatacagagattttgtttttatatc----ttatatgtggtcctaaaattatattgat--tcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCTGGTTTTGCACCCTATGAAAAGCGTATAACTGAGTTGCTGAAGGTTGGGA
   | || | |   ||  |   |||||  |  |   ||| | || |  |||| |||| |  |     || | ||||  | | |   ||  || ||  |  |  |||||| |||  |||||||||  | | || |||  ||| || |||||||||||||| ||||| || ||||| |||||||| || ||| | ||||||||||| |
--cacttgtaaa--tggctcatataaatctggt--ggacttgcatatgtttttttttcacttgatgattttctgtgccctttattgtaacttcatggtgtattcagAAAGCAACGAAGAGGGTGTCCATGGTCAGGGGCCTGATCAGAGAGGTTGCTGGCTTTGCTCCTTATGAGAAGCGTATCACCGAGCTTCTGAAGGTTGGCA

upper sequence: GLYMA10G37840.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g00610.t01 (Vitis vinifera), 3'ss of exon 2
----ttaaattatgatgctgtattggataaaaataattaagaca--tacagagattttgtttttatatcttatatgtggtcctaaaattatattgattcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCTGGTTTTGCACCCTATGAAAAGCGTATAACTGAGTTGCTGAAGGTTGGGA
    ||||||||   |  | | ||   ||    |  ||||||    || |  || |    | | ||    |  || ||||  ||    | | | | |   |  |||||||| ||||||||||| || || || |||||| | || || || ||||||||||||||||| ||||| ||| | || |||||| | || || |||||||
atggttaaattacagtttttttttaatta---ttttttaagattgttatatggaataaagtgtcattatgttcat-tggt--tacccctttttgggtgtcattcagAAAACCAGCAAGAGGGTCCATTTCGTAAGGAACTTGATCAGGGAAGTTGCTGGTTTTGCACCATATGAGAAGAGAATCACTGAGCTTCTCAAAGTTGGGA

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|120533486|gb|EH261619.1|EH261619
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|19269736|gb|BM885992.1|BM885992
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|213618406|gb|DB961579.1|DB961579
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|17021112|gb|BM092146.1|BM092146
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|120494562|gb|EH222729.1|EH222729
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|4287211|gb|AI441157.1|AI441157
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|42722526|gb|CK768425.1|CK768425
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|15663379|gb|BI700750.1|BI700750
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|21601409|gb|BQ611740.1|BQ611740
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|58022088|gb|CX708829.1|CX708829
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|151396437|gb|EV266314.1|EV266314
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|7042161|gb|AW472055.1|AW472055
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTTATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|18730445|gb|BM525882.1|BM525882
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|16342062|gb|BI967657.1|BI967657
EST:     ATGTCGTCCCCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGANNCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|151412115|gb|EV281927.1|EV281927
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|7232950|gb|AW568301.1|AW568301
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|7232862|gb|AW568214.1|AW568214
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|15664968|gb|BI702339.1|BI702339
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|31474246|gb|CD416274.1|CD416274
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|11689158|gb|BF596834.1|BF596834
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|120531718|gb|EH259851.1|EH259851
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|21889217|gb|BQ742430.1|BQ742430
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|254341148|gb|GR854876.1|GR854876
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|24136180|gb|BU926690.1|BU926690
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|31456593|gb|CD398621.1|CD398621
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|58014661|gb|CX701403.1|CX701403
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
EST: gi|31311388|gb|CD396591.1|CD396591
EST:     ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGG                         AAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT
genomic: ATGTCGTCACCAAGAAGGAATTGCCCCCACGCCCCTCGGATCGTAAGGGGgtaagttttt ... ttcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattttgtttttatatcttatatgtggtcctaaaattatattgattcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCTGGTTTTGCACCCTATGAAAAGCGTATAACTGAGTTGCTGAAGGTTGGGA
                               taaaattatattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaattatgatgctgtattggataaaaataattaagacatacagagattttgtttttatatcttatatgtggtcctaaaattatattgattcaaaacagAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATAAGAGAGGTTGCTGGTTTTGCACCCTATGAAAAGCGTATAACTGAGTTGCTGAAGGTTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - tgatgct
- - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - -acataca