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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgagaagggtttaatgttctgaagttttgccgtgcttaagttttcattctttcatgtttaatatgcttgtgagctgttaatattatgattgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG

Basic information

species Glycine max
transcript GLYMA11G08390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 3
agtgagaagggtttaatgttc--tgaagttttgccgtgcttaagttttcattctttcatgtttaatatgcttgtgagctg--ttaatattatgattgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG
    |  | | ||  |||| |  ||   | |     ||  | | ||   |||  |  |    |  |||| |    | |||  ||  | || |   ||   | || || |||||||| ||||||||||| || ||||| ||||| || || |||||||| || || |||||||| || ||||| || ||||| || ||||| || 
---aatcatgcttgcatgtacaatgggatgtgattttgactcatttgaaattgctgaagaactgttatggtatgaacctgatttggtgttgttcatgtcct-agCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCCTGCGAAAGACGTTCTTAAAGACCTTGTTGAAATGTGTCGAGGCATCCAA

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 3
--agtgagaagggtttaatgttctgaagt-tttgccgtgcttaagttttcattctttcatgtttaatatgcttgtgagctgttaatattatgattgca-atcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG
    |||  |    | ||  || |||||   |   | |  || |    | || | |  ||| ||  ||||        |   | || |  || || ||   ||| || ||||| || || || ||||| || ||||||||||| || || |||||||| || ||||||||||| ||||| || || |||||||| |||||||||
ctcttgaacatctatgaaatttatgaagagctaatcttttttcaaggataatacct--atgatt--tatgaaaacatacatctgatttggtgtttacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAG

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 3
---agtgagaagggtttaatgttctgaagttttgccgtgcttaagttttcattctttcatgtttaatatgcttgtgagctgttaatattatgattgca-atcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG
     |||  |    | ||  || |||||   ||   | |||        || | |  ||| ||  ||||        |   | || |  || || ||   ||| || ||||| || || || || || || ||||||||||| || || |||||||| || ||||||||||| ||||| || || |||||||| |||||||| 
gctcttgaacatctatgaaacttgtgaagaactgatcttcttctaggagaatacct--atgatt--tatgaaaacatacatcttatttggtgtttacatgccagCTATCTCCTGTGCACGGTGGGGTCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAA

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 3
agtgagaagggtttaatgttctgaagttttgccgtgcttaagttttcattctttcatgtttaatatgcttgtg-agctgttaatattatgattgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG
      |||  | |  ||||||    | |||    |  || ||| |||||    ||   | | | |   | || || |  | ||    ||| |    ||||||| ||  | |||||  ||||||| ||||| |||||||||||||| | | |||| | |||| | |||||||||||||| || ||||| || |   |||| 
----gtaagtttcttttgttct----tgttgttcagaatacgttgtcatttgcacactctgattttaactttgtagatactcatcaattgagtt---tcagGTATCTTTTATGTACCATAGGATCTGTATATATCAAATCCAAGGATGTTACTGCTACGGATATACTTAAGGATCTTGTTGAAATGTGTCGAGCTGTTCAA

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 3
agtgagaagggtttaatgttctga--agttttgccgtgcttaagttttcattctttcatgtttaatatgcttgtgagctgttaatattatgattgcaatc--agGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG
  |||  |    || |||||   |  | || | | |   || ||| |     |||   |   |||  |  |    |  |||| || ||||  |  |   |  ||||| ||||| ||||||| |||||| || || |||||| |||||||||||||||| |||||  ||||||| |||||||| |||||||||||||| ||||||
tttgattactacttgatgttgctagcatttcttctgatatttagtctgttcacttctctagctaaagtaat----atttgttcattttattttcccttccctagGTATCTCCTATGTACAGCAGGATCCGTGTATATCAAAACCAAGGAAGCTCCTGCCAAGGAAATTCTTAAAGATCTTGTTGAGATGTGCCGTGGGATTCAG

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 3
agtgagaagggtttaatgttctgaagtt-ttgccgtgcttaagttttcattcttt-catgtttaatatgcttgtg--agctgttaatattatgattgcaat----cagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG
        || ||  |  || |  ||   |     ||  ||| |||| ||| ||| |||||    | | | |||   |  | | |||  | || |  | ||    |||||| || ||||||||||| ||||| || ||||||||||| ||||| |||||||| |||||||||||||||||||||||||| |||||||||||||| || 
--------ggattgtacattatagagacatcagtttgtataaatttttatttttttcatgtaatgtttccatgtcttaattttgaattctgtgttctctattgcccagGTATCTTCTCTGTACAGTTGGATCTGTGTACATCAAATCTAAGGAGGCTCCTGCTAAGGATGTTCTTAAGGATCTTGTGGAAATGTGCCGTGGCATCCAA

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ33136 (Selaginella moellendorffii), 3'ss of exon 3
agtgagaagggtttaatgttctgaagttttgccgtgcttaagttttcattctttcatgtttaatatgcttgtgagctgttaatattatgattgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG
                                  ||||    || |  ||||    | | |   || ||  ||||  ||        |  || |  |||||||||| ||   ||||||||| || || ||||| || |||||||||||||| |||||||| || || |||||| | || || ||| |||||||  | |||
-------------------------------gtatgctctttttctttttctactctttctttcattctcctgagacgtcgt-----tcgtttctttcagGTACCTGCTTATTACAGTAGGCTCGGTGTACATAAATTCCAAGGAAGCTCCCGCAAAGGACGTCCTGAAGGATTTGGTTGAAATGAGCCGTGGTGTCCAG

upper sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ27365 (Selaginella moellendorffii), 3'ss of exon 3
agtgagaagggtttaatgttctgaagttttgccgtgcttaagttttcattctttcatgtttaatatgcttgtgagctgttaatattatgattgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG
                           | |||  |  ||   ||| || ||||||   |||   || ||  ||||  ||        |  || |  |||||||||| ||   ||||||||| || || ||||| ||||||||||||||||| |||||||| ||  | |||||| | || || ||| |||||||  | |||
--------------------------gtatgctctttttctttttccactctttc---ttt--cattctcctgagacgtcgt-----tcgtttctttcagGTACCTGCTTATTACAGTAGGCTCGGTGTACATAAAATCCAAGGAAGCTCCCGCAAAGGACGTCTTGAAGGATTTGGTTGAAATGAGCCGTGGTGTCCAG

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|193342684|gb|FK306510.1|FK306510
EST:     ATTGATCTTTATGAACTCGTCCAGCACGCCGGCAACATTTTGCCCCGATT                         GTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCC
genomic: ATTGATCTTTATGAACTCGTCCAGCACGCCGGCAACATTTTGCCCCGATTgtaagtggca ... ttgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCC
EST: gi|254342605|gb|GR858767.1|GR858767
EST:     ATTGATCTTTATGAACTCGTCCAGCACGCCGGCAACATTTTGCCCCGATT                         GTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCC
genomic: ATTGATCTTTATGAACTCGTCCAGCACGCCGGCAACATTTTGCCCCGATTgtaagtggca ... ttgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCC
EST: gi|15285344|gb|BI469235.1|BI469235
EST:     ATTGATCTTTATGAACTCGTCCAGCACGCCGGCAACATTTTGCCCCGATT                         GTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCC
genomic: ATTGATCTTTATGAACTCGTCCAGCACGCCGGCAACATTTTGCCCCGATTgtaagtggca ... ttgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCC
EST: gi|120531471|gb|EH259604.1|EH259604
EST:     ATTGATCTTTATGAACTCGTCCAGCACGCCGGCAACATTTTGCCCCGATT                         GTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCC
genomic: ATTGATCTTTATGAACTCGTCCAGCACGCCGGCAACATTTTGCCCCGATTgtaagtggca ... ttgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattctttcatgtttaatatgcttgtgagctgttaatattatgattgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG
                               tgttaat  putative branch site (score: 3)
                               tgttaatattatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgagaagggtttaatgttctgaagttttgccgtgcttaagttttcattctttcatgtttaatatgcttgtgagctgttaatattatgattgcaatcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - ttttgcc
- - - - - - - - - - - - - - - - -gtgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgtta