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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttcacaacaattgatgttacatactatcattttaattctgatcaatataatttgtttagcatttatgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG

Basic information

species Glycine max
transcript GLYMA10G06590.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 4
gtaaatttcacaacaattgatgttacatactatcattttaattctgatcaatataatttgtttagcatttatgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG
||||   |    | ||   || | |  | | ||   | |  ||   || | |      ||| |   ||||||      ||||||||||| |||||||| |||||  | ||||| || || || |||||||||||||| || || ||||||||||| |||||||||||| |  ||||  | |
gtaagcattcttaaaagcaatatcattttc-attggtcttgttagcattattcatcactgtgtgctatttatt--ctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG

upper sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 3
gtaaatttcacaacaattgatgttacatactatcattttaattctgatcaatataatttgtttagcatttatgg-gtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG
||||   |    | ||  |||||| | | | || ||| | |   ||||   | |  ||    | |  || ||      ||||||||||||||||||||| |||||| | ||||| |||||||| ||||||||||| || || || ||||||||||| || |||||||||||  ||||  | |
gtaagcattctta-aagagatgttgctt-caattattgtcaccatgat---tctttttcaccttgtcttaattccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGTTTGAGAGTGGCAGAGTATGCTTTCCATTATGCCAAGGCCAATGGCCGGG

upper sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 3
gtaaatttcacaacaattgatgttacatactatcattttaattctgatcaatataatt--tgtttagcatttatgggtctc-----agGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG
||||   |    | ||  |||||| | | | || ||| | | | || |||  || |||  | || | | | |    || ||     |||||||||||||||||||||||||| | ||||| ||||| || ||||||||||| || || || || ||||||||||| |||||||||||  ||||  | |
gtaagcattctta-aagagatgttgctt-caattattgtcagtttg-tcagcatgattctttttcaccctgtcctagtttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGTTTGAGAGTGGCAGAATATGCTTTTCATTATGCCAAGGCCAATGGCCGGG

upper sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 2
-----gtaaatttcacaacaattgatgttacatactatcattttaattctgatcaata----taat-------ttgtttagcatttatgggtct--cagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG
     ||   ||| |   | ||||||   | ||   |   |  |  |||| || |||     ||||       ||||||     | | |  | |   ||||||| |||||||| || |||||||| ||||||||||| ||||| || ||||| || || || ||||||||||||| |||||||||| ||||||||||||
gtttagtttgttttaagtctattgatcgaatatttcaggttagttcttctaataaatgattctaatgatggttttgttttctcctgacgcatataatagGTTGTTAGAGGTGTGGTGGAAAGTCTTAAAATCATTACCCGTCAGGCGAGTTTGAGAGTTGCAGAGTATGCTTTTCTCTATGCCAAGACTCATGGAAGAG

upper sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 2
----gtaaatttcacaacaattgatgttacatactatcatt--ttaattctgatcaatataatttgtttagcatttatgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG
    ||   |||||  |  ||| |     |||   |  | |  ||||| |  |  ||| | |    |||    |  || |||  ||||| ||| ||||||| || ||||| |||||||| ||||| ||||| || ||||| ||||| ||||||||||| ||||||||||||||| | ||||||||||
gtgagttgttttcaagaggatttaatgctcatctgacaaatacttaatgcatagaaatttgaaggatttcttgta-attggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGTTTGAGGGTGGCTGAGTATGCATTTCACTATGCCAAGACCCATGGAAGAG

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|192302073|gb|FG993457.1|FG993457
EST:     TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         -TTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|254329852|gb|GR839405.1|GR839405
EST:     TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAT                         GTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|14259098|gb|BG882006.1|BG882006
EST:     TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|151393897|gb|EV263768.1|EV263768
EST:     TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|19268871|gb|BM885127.1|BM885127
EST:     TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|213602099|gb|DB962592.1|DB962592
EST:     TTACAATTCGTGAAAATACTGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|209725272|gb|BW672747.1|BW672747
EST:     TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTCTCAGAATCATTACACGTCAAGCAAGT
genomic: TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|192328451|gb|FK020725.1|FK020725
EST:     TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|209700402|gb|BW664415.1|BW664415
EST:     TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAN                         GTTGTGAGNAG-TGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAG
genomic: TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtctcagGTTGTGAG-AGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAG
EST: gi|8286498|gb|BE024057.1|BE024057
EST:     TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|10233963|gb|BE802851.1|BE802851
EST:     TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|298171951|gb|HO021543.1|HO021543
EST:     TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTTGTAGAAAGTCTC
genomic: TTACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactatcattttaattctgatcaatataatttgtttagcatttatgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG
               ttctgat  putative branch site (score: 3)
        attttaattctgatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttcacaacaattgatgttacatactatcattttaattctgatcaatataatttgtttagcatttatgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA