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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG

Basic information

species Glycine max
transcript GLYMA15G18170.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 3
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
                                     | | | |  ||  |   |       | ||||||||| |    ||    |  ||    | |      | ||     | || ||||||||||||||| | ||||| || ||||||||  ||||||||||||| ||||| |||
------------------------------------gtgagaaactataccgctacggcttaaaattgtctttgtttgcataa--gcattgacagttcgctatgcttt----atgt-agTATCAATGCCATGCACCCCAAGACCAGGAAGATCTTGCAGCTTCTGCGGTTGAGGCAG

upper sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 3
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
                               |  |   ||    | ||| ||  ||  |         | | | || ||||  ||||||||      |||  ||||   | |||  |||||||||||||||| |||| || || ||||||||  ||||||||||||||||||| |||
-----------------------------gtgagtcgcaagtgcttatgccagtattatgtagaggaatttgtatgattatgcttgttttt------aattccgtt---gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG

upper sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
                  || || | || || ||||   || |  || |  || |   |  | | ||   | | |   | || |   |  | || |||      | | | || | |||||||||||||||| || || || |||| ||||||| |||| ||| ||||||| ||||||
-----------------gtaata-tgatctactattactatctcccaag-tataaggatgatgtgttacttctataactgttttc--tcatttttctatctatttgtttctatcatcagTATCAATGCCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTTAAGACAG

upper sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
                ||| |||      || | || |  | | || |   | ||| |    |    || | | ||    |||||||| || |  ||  ||   ||| |   |   ||||||||||||||| || || || || | ||||||||| |||||  ||||||||||||||
---------------gtatgtta------tactgttgttgtttgtcttataagcatttctaaagccagtgtctatg----ttgttgttcttat--ctgttgttctttttaatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG

upper sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
                     ||  |   || |||||   | |  ||| |  |  |     || ||| | |||||  ||   ||  || ||        || | |||         ||||||||||||||| || || ||||| | ||||||||||||||| |||||||||||||||
--------------------gtatgtgcctattatttgtgtgttacataagttgttgcatatagattctgttttttatttacgtgattgtt--------tgtcatttg--------cagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG

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|151410194|gb|EV280009.1|EV280009
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|22932168|gb|BU549307.1|BU549307
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGNNN
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|192327716|gb|FK021351.1|FK021351
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|17023603|gb|BM094637.1|BM094637
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|192295535|gb|FG988109.1|FG988109
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|8282865|gb|BE020426.1|BE020426
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|10232891|gb|BE801779.1|BE801779
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAAGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|58021409|gb|CX708150.1|CX708150
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAACCAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|151400307|gb|EV270121.1|EV270121
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|31306158|gb|CD391361.1|CD391361
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCCAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|58015969|gb|CX702711.1|CX702711
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|298195246|gb|HO043774.1|HO043774
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|209702466|gb|BW667098.1|BW667098
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|33388304|gb|CA851511.1|CA851511
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|209728367|gb|BW660005.1|BW660005
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|15663868|gb|BI701239.1|BI701239
EST:     GTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: GTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|192294770|gb|FG986619.1|FG986619
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|9820878|gb|BE556388.1|BE556388
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|151404968|gb|EV274782.1|EV274782
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|12689954|gb|BG156290.1|BG156290
EST:     TCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|151395296|gb|EV265167.1|EV265167
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|192307998|gb|FG998981.1|FG998981
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|58024451|gb|CX711192.1|CX711192
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|16996376|gb|BM085748.1|BM085748
EST:     CGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: CGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|8284546|gb|BE022114.1|BE022114
EST:     GTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: GTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|57574809|gb|CX547784.1|CX547784
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|192307999|gb|FG998982.1|FG998982
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
                                        tttctgt  CT-rich tract
             ttattgttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT