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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaattccactgcatttttgtgtaaatcatggtgtttattgtcctgatgctggtatcaatctttaactgtatatttaaactagtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCAAGGGACTTGACGTTATACAACAGGCCCAGTCTGGAACTGGGAAAACAGC

Basic information

species Glycine max
transcript GLYMA09G07530.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 3
---------------caaattccactgcatttttgtgtaaatcatggtgtttattgtcctgatgctggtatcaatctttaactgtatatttaaactagt--ttgatttgtg-------ttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCAAGGGACTTGACGTTATACAACAGGCCCAGTCTGGAACTGGGAAAACAGC
                 || |  |     |||      | | | |  ||||| || |  ||    |  ||| ||  ||    | | |  |    |  ||  |||||| ||        || ||||||| || ||||| || |||||||||||||| ||||| || || || |||||||| ||||| || || || ||||| |||||||| ||||| ||||| ||
gtatctatgcttacggtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAGTCTGGTACTGGAAAAACCGC

upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13920.4 (Arabidopsis thaliana), 3'ss of exon 3
----caaattccactgcatttttgtgtaaatc--atggtgtttattgtcctgatgctggtatcaatctttaactgtatatttaaactagtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCAAGGGACTTGACGTTATACAACAGGCCCAGTCTGGAACTGGGAAAACAGC
      |     |  | || | |||   ||    |    | |   | |  ||||    || | |   |  |||  |||  | |  |  | ||   || | | ||||||||||||||||| || |||||||||||||| ||||| || || ||||| ||||| ||||| || || |||||||| |||||||| ||||||||||||||
gtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattat-ctcatgcgtgcttctgttttttcttagGTTTTGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATCGTCCCCTTCTGTAAGGGTCTTGATGTGATTCAACAGGCTCAGTCTGGTACTGGGAAAACAGC

upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 3
caaattccactgcatttttgtgtaaatc--atggtgtttattgtcctgatgctggtatcaatctttaactgtatatttaaactagtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCAAGGGACTTGACGTTATACAACAGGCCCAGTCTGGAACTGGGAAAACAGC
           | || | |||   ||    |    | |   | |  ||||    || | |   |  |||  |||  | |  |  | ||   || | | ||||||||||||||||| || |||||||||||||| ||||| || || ||||| ||||| ||||| || || |||||||| |||||||| ||||||||||||||
-----------gtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattat-ctcatgcgtgcttctgttttttcttagGTTTTGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATCGTCCCCTTCTGTAAGGGTCTTGATGTGATTCAACAGGCTCAGTCTGGTACTGGGAAAACAGC

upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------caaattccac---tgcattt-ttgtgtaaatcatggtgtttattgtcctgatgctggtatcaatcttta--actgt-atatttaaactagtttg-atttgtgtt-----------ttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCAAGGGACTTGACGTTATACAACAGGCCCAGTCTGGAACTGGGAAAACAGC
                         || |||| |    | | ||  |||| |   ||  | | | |||| | ||  || | || ||||   |||  ||||| |   |||||| |  |   ||| || ||           |||||||| |||||||| || |||||||||||||| |||||  |||||||||||||||| ||||| || || || || || || ||||||||||| || || ||
gtaagtgaagtatttcctttgagaacacattctatacataccttcattgtttctgtctagttttgtatt-ttcttttgtttgtttcaaagcttagtactgttactcttaaacaacctcatattggttttgttatttatcattagGTTTCGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATTATTCCATTCTGCAAGGGTCTTGATGTGATCCAGCAAGCTCAATCTGGAACTGGAAAGACCGC

upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54270.1 (Arabidopsis thaliana), 3'ss of exon 3
caaattccactgcatttttgtgtaaatcatggtgtttattgtcctgatgctggtatcaatctttaactgtatatttaaactagt--ttgatttgtg-------ttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCAAGGGACTTGACGTTATACAACAGGCCCAGTCTGGAACTGGGAAAACAGC
  || |  |     |||      | | | |  ||||| || |  ||    |  ||| ||  ||    | | |  |    |  ||  |||||| ||        || ||||||| || ||||| || |||||||||||||| ||||| || || || |||||||| ||||| || || || ||||| |||||||| ||||| ||||| ||
gtaagtgaagaaggtttaaagaaacaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAGTCTGGTACTGGAAAAACCGC

upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 3'ss of exon 2
caaattccactgcatttttgtgtaaatcatggtgtttattgtcctgatgctggtatcaatctttaactgtatatttaaactagtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCAAGGGACTTGACGTTATACAACAGGCCCAGTCTGGAACTGGGAAAACAGC
   ||     |   |||| ||| ||||     |   |    |  |  |||     |||       ||  |  ||| |||   |  | |||  |  | |||||||||| || || || || ||||||||||| ||||| ||||| || |||||||||||||| || || || || || ||||| ||||| || || || ||
tgtatattgatatgttttcgtgaaaatttcttttcctccgtttgttttgcattgctcatgtcagtaccatcaattgaaagatggataattcttcgtgtagGTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCAAGGGACTTGATGTAATTCAGCAAGCTCAGTCAGGAACAGGAAAGACTGC

upper sequence: GLYMA09G07530.3 (Glycine max), 3'ss of exon 3
lower sequence: PP1S31_150V6.5 (Physcomitrella patens), 3'ss of exon 3
caaattccactgcat-ttttgtgtaaa-tcatggtgtttattgtcctgatgctggtatcaatctttaactgtatatt--taaactagtttgatttgtgttt-------tagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCAAGGGACTTGACGTTATACAACAGGCCCAGTCTGGAACTGGGAAAACAGC
          ||||| |||||||     |  |||||||  | ||       |  | | ||||  | ||| | |   |  |   ||| | | |||   |||         |||||||||||||||||| ||||| || ||  | ||||| ||||| |||  |||||| ||||| || || ||||| ||||||||||||||||| || |||||
---------ttgcatgttttgtgggtgcttgtggtgttcgtagtttcctaccgagaaccaat--tgaaccgcactctgctgctctaatctcattctggttgacctgtacagGTTTTGAGAAGCCATCTGCTATCCAACAGCGTGGAATCGTTCCCTTCACCAAGGGTCTTGATGTCATTCAACAAGCCCAGTCTGGAACTGGCAAGACAGC

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|12774537|gb|BG239464.1|BG239464
EST:     CTATGGGCTGGCAAGAGAATCTGCTGAGAGGCATCTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
genomic: CTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
EST: gi|213602164|gb|DB962657.1|DB962657
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
EST: gi|298164132|gb|HO013777.1|HO013777
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
EST: gi|7685921|gb|AW756569.1|AW756569
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
EST: gi|213587858|gb|DB959682.1|DB959682
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
EST: gi|24136576|gb|BU927086.1|BU927086
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
EST: gi|213596258|gb|DB960215.1|DB960215
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
EST: gi|23728371|gb|BU762237.1|BU762237
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
EST: gi|209713719|gb|BW681859.1|BW681859
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
EST: gi|19268988|gb|BM885244.1|BM885244
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAAGGGAATAGTTCCATTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
EST: gi|16347853|gb|BI973448.1|BI973448
EST:     TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA
genomic: TGATGCTATGGGCTTGCAAGAGAATCTCCTGAGAGGCATTTATGCATATGgtagatttaa ... tgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgctggtatcaatctttaactgtatatttaaactagtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCAAGGGACTTGACGTTATACAACAGGCCCAGTCTGGAACTGGGAAAACAGC
            aatctttaactgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaattccactgcatttttgtgtaaatcatggtgtttattgtcctgatgctggtatcaatctttaactgtatatttaaactagtttgatttgtgttttagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGAATAGTTCCATTCTGCAAGGGACTTGACGTTATACAACAGGCCCAGTCTGGAACTGGGAAAACAGC

- - - -cactgca
- - - - - - - -ttttgtg
- - - - - - - - - - - - - -catggtg
- - - - - - - - - - - - - - - - - - - - - -ctgatgc