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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgtcccttctatatgagtgtctccatggattgcagaatatatctgcagagataattatttagatgtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG

Basic information

species Glycine max
transcript GLYMA12G15470.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 8
-------gtgatgtcccttctatatgagtgtctccatggattgcagaatatatctgcagagataattatttagatgtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG
         ||  | || |  |  |     | | |    | |   || |||             |   ||      | |||||| ||||||||||||| ||||| || |||||||| ||||| |||||||| || |||||||||||||| || || ||||| |||||||| ||||||||||||
gtactgcaagacatgccatgcagttctaattttgctcctactattgagtatgggcatcttctctaaccttgtatgatattcttgcagGTTCTTGGTACACCAACCCGTGAGGAAATACGTTGCATGAACCCGAACTATACAGAGTTTAGGTTTCCACAGATAAAAGCTCACCCTTGGCACAAG

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 8
gtgatgtccctt-ctatatgagtgtc--tccatggattgcagaatatatctgcagagataattatttagatgtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG
||  ||     |  | |   ||   |  |   |   ||||      ||| |   | | ||| |   ||      || | | ||||||||||||||||||| || |||||||| || || |||||||| || ||||| ||||| | ||| ||||||||||| ||||||||||||||||||
gtattgcatgatgttgtgcaagctacatttttttttttgccacgggtatttcttgtgttaacttgata------ttatggcagGTTCTTGGTACTCCAACCCGTGAGGAAATACGATGCATGAACCCCAACTATACTGAGTTCAAATTTCCTCAGATTAAGGCTCATCCTTGGCACAAG

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 8
gtgatgtcccttctatatgagtgtctccatggat-tgcagaatatatctgcagagataattatttagat------gtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG
          | ||  |  | |||  | | | |        ||   ||| | | | |  || ||  | |       | | | |||||||||||||||||||||| || ||||| || || || ||||| || || ||||| ||||| || || |||||||| || |||||||| |||||||||
---------gtactgca-aaatgttccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAG

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
gtgatgtcccttctatatgagtgtctccatg-gattgcagaatatatctgcagagataattatttagat------gtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG----
          | ||  |  | |||  | | |          ||   ||| | | | |  || ||  | |       | | | |||||||||||||||||||||| || ||||| || || || ||||| || || ||||| ||||| || || |||||||| || |||||||| |||||||||    
---------gtactgca-aaatgttccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
gtgatgtcccttctatatgagtgtctccatgga--ttgcagaatatatctgcagagataattatttagatgtctt---cttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG
          |  |  |  |   ||   || ||  ||  |        | ||   | || |||||   ||||  |   | |||||||||||||||||||||| || ||||| || || || ||||| || || ||||| ||||| || || |||||||| || |||||||| |||||||||
---------gtattgcaaaatgttccaaatagaaattctattcctctgccgcgacgttacttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgatgtcccttctatatgagtgtctccatggattgcagaatatatctgcagagataattatttagatgtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG
||||    | |  | ||| |   | |   | |    ||     | ||||    | | || || | | ||| ||  | |||||||||||||||||||| ||||| |||||||| || ||||||||||| || ||||| || |||||||| || || ||||| || |||||||| |||
gtga-actcttcttttattatattttgttttggcgtcatttcctgtctgt---gctcatgatgt-gctgtgttggtttagGTTCTTGGTACTCCAACTCGCGAAGAAATCCGGTGCATGAACCCAAACTACACAGACTTCAGATTCCCACAAATCAAAGCCCACCCTTGGCATAAG

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------gtgatgtcccttctatatgagtgtctccatggattgcagaatatatctgcagagataattat-ttagatgtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG
                             ||| | |   || | | || || |     | || |  ||  || || ||     |||| ||   | | |  ||| || |||||||||||||||||||| || || ||||| || ||||||||||| || || ||||| ||||| ||||| || || |||||||| ||||||||||||
gtgaagtctcctttattagactaatggatgtgctcttttttgtctttg-gtattagactagaatctag--taaatatgttaccataagtacacttgctaccttgttttagGTTCTTGGTACTCCAACTCGTGAAGAAATTCGATGTATGAACCCGAACTACACAGATTTTAGGTTCCCACAAATCAAAGCTCACCCTTGGCACAAG

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
--gtgatgtcccttctatatgagtgtctccatggattgcagaatatatctgcagag--ataattatttagatgtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG
  |     ||  |||| | |   | |   |  ||||       |||  |      |   ||||   | |    | ||||  ||||||||||||||||||||  | || ||||| || ||||||||||| |||||||| || || || || |||||||| |||||||||||||||||||||
gtgcagcatcatttct-tgttgatattatcgaggatcatctgctatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
gtgatgtcccttctatatgagtgtctccatggattgcagaatatatctgcagagataattatttagatgtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG
         |   |  ||   || |||  |   ||      | | |  |    | |  |  |  |||  |  | ||| ||||  | |||||||| || ||||||||||||   || ||||| ||||| || || |||||||  ||||||||||||||||| ||||| |||||||||
------gtacgcatgcattcttg-ctcttttttttctgttttttttgcgagtcgctcttgctcaagacttgcttttgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
gtgatgtcccttctatatgagtgtctccatggattgcagaatatatctgcaga--gataattatttagatgtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG
               || |  ||  | | ||   |      | | | |||     | |  |  |  |||  |  | ||| ||||  | |||||||| || || |||||||||   || ||||| ||||| || || |||||||  ||||||||||||||||| ||||| |||||||||
--------------gtacgcatgcattcttgctctcttttttctttttgcgagtcgctcttgctcaagacttgcttttgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

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|208212469|gb|GE011822.1|GE011822
EST:     CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAG                         GTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
genomic: CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAGgtgatgtccc ... cttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
EST: gi|10237492|gb|BE806380.1|BE806380
EST:     CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAG                         GTTCTTGGTACTCCAACACGCGAAGAAATCCGTTGTATGAACCCAAATTAT
genomic: CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAGgtgatgtccc ... cttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
EST: gi|16996079|gb|BM085451.1|BM085451
EST:     CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAG                         GTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
genomic: CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAGgtgatgtccc ... cttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
EST: gi|193713415|gb|FK651922.1|FK651922
EST:     GTGGAAATTATCAAG                         G-TCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
genomic: GTGGAAATTATCAAGgtgatgtccc ... cttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
EST: gi|193532704|gb|FK489794.1|FK489794
EST:     CAACTTGTGGAAATTATCAAG                         GTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
genomic: CAACTTGTGGAAATTATCAAGgtgatgtccc ... cttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
EST: gi|208260673|gb|GE059429.1|GE059429
EST:     GAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAG                         GTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
genomic: GAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAGgtgatgtccc ... cttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
EST: gi|193404932|gb|FK373359.1|FK373359
EST:     ACCAACTTGTGGAAATTATCAAG                         GTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
genomic: ACCAACTTGTGGAAATTATCAAGgtgatgtccc ... cttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
EST: gi|208284980|gb|GE086942.1|GE086942
EST:     CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAG                         GTTCTTGGTACTCCAACACGCGAGGAAATACGTTGTATGAACCCAAATTAT
genomic: CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAGgtgatgtccc ... cttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
EST: gi|208074942|gb|GD875439.1|GD875439
EST:     CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAG                         GTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
genomic: CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAGgtgatgtccc ... cttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
EST: gi|193690271|gb|FK634568.1|FK634568
EST:     CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAG                         GTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
genomic: CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAGgtgatgtccc ... cttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
EST: gi|22525206|gb|BU084017.1|BU084017
EST:     CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAG                         GTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
genomic: CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAGgtgatgtccc ... cttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
EST: gi|19935688|gb|BQ080542.1|BQ080542
EST:     CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAG                         GTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT
genomic: CATTATTTCCTGGAGAAAACCAAGTGGACCAACTTGTGGAAATTATCAAGgtgatgtccc ... cttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatggattgcagaatatatctgcagagataattatttagatgtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG
                                          tgtcttctt  CT-rich tract
                           agataattatttagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgtcccttctatatgagtgtctccatggattgcagaatatatctgcagagataattatttagatgtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA