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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtaggagcatcagttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtacatatattttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG

Basic information

species Glycine max
transcript GLYMA15G01680.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
ggtaggagcatcagttctcattcatttgccttgtttgagtagtct--tatcatgttgacga--------gtggct--catggattaaagagagtacatatattttat-tgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
 |||    | | |  |     || | |   |   ||||  ||| |  |  |||   ||  |        ||   |    ||| || |       | || |   || | | |||||||||||||||||||| || ||  |||| ||||||   || ||||||||||| |||||||| ||||||||||||||  |||| |||   || | ||   
-gtaatttcttaatcttctgctcttatctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT

upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
----ggtaggagcatcagttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtacatatattttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
      |   ||  | |     || |  |||   ||||  |||   | |  |  | ||  |        | |   ||        | |   ||| ||  |  |||| || || ||||| || ||||||||||| |||||||| || || ||||| ||||||||||| |||||  |||| ||   ||| ||| |||| |  | | 
tcttattttcagacttacgcgacact-gtttaatttgtaggagctatgt-gttttattatctcaccatgccttttttccttctcatgccattatctt--tatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC

upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 20
ggtaggagcatca-gttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatgga------ttaaagagagtacatatattttat-tgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
 |||    | | | ||||||||     |    | | |||  ||| |  |    ||    |      ||||        |||       |   | ||  || | ||||| |||||||||||||||| || ||  |||| ||||||   |||||||||||||| |||||||| ||||||||||| ||| |||| |||   |  | ||   
-gtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtggtgccattagaaaaaaatgcatgctattatcttattctttttttctgtaccttgtatgcagATTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAATATCCAAATTTATTTGAAGACTGGCAGGTTGCTCTAACTGTAGAAAAAAGCGTTGCTT

upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 6
ggtaggagcatca-gttctcattc--atttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtacatatattttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
 |||    | | | ||||||||     | | | || |   |   ||| | ||||  | |  |      ||||   | |    | |   | | | |   ||||| |||||||||||||||| || ||  | || ||||||   |||||||||||| | |||||||| ||||||||||| ||| |||| |||   |  | || | 
-gtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtcatgtcattataaaaaaaactgcatgctattatcttattctttttgtctgtatgcagATTAATCCAAAAGCTGCAGAGTCTCTAGCAGATCCTTCTGAATATCCAAATCTATTTGAAGACTGGCAGGTTGCTCTAACTGTAGAAAAAAGTGTTGCGT

upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 21
ggtaggagcatca-gttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggct-catggattaaagagagtacatatattttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
 |||    | | | ||||||||     |    | | |||  ||| |  |    ||    |    || ||||   | |    | |   | | | |   ||||| |||||||||||||||| || ||  | || ||||||   |||||||||||| | |||||||| ||||||||||| ||| |||| |||   |  | || | 
-gtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtcgtgtcattagaaaaaaactgcatgctattatcttattctttttgtctgtatgcagATTAATCCAAAAGCTGCAGAGTCTCTAGCAGATCCTTCTGAATATCCAAATCTATTTGAAGACTGGCAGGTTGCTCTAACTGTAGAAAAAAGTGTTGCGT

upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 21
ggtaggagcatcagttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtacatatattttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
          |   ||   | || |||    | || | ||| | |  ||| |  ||| ||| |    ||| || |||  |   | |  | || | | ||||||||| ||||||| || ||||| |||||||||||||| || ||  ||||| | |||||||||||||| ||||| ||  |||| ||| |||||||||| |
---------gttcctttcaaatctttttaggttttagtgtaatgtggtcaaggagacaagttg----tgggtttaagttac--cttgcacttgaatacagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG

upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 21
ggtaggagcatcagttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtacatatattttattg-cagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
             ||| |  |||   |   || ||||  || | |    |||   |       |   ||| || ||   | | | | |   || |   ||||||||||||||||| |||||||| || |||||||||||||| ||  ||||| | ||||| |||||||| ||||| ||  |||| ||| | ||  |||  |
-------------gttatt-ttcgcatcttttttttgtttactgtgtcaatgagaaaattcatcatgtggctttaa---attgcctttgacttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG

upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 21
ggtaggagcatcagttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtac-atatattttat-tgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
  || |       |      |  || |   |  ||| | |  |||| | || || | ||  |   ||   ||  ||    ||   ||  |   ||| |||||||||||||||||||||||||||| ||||||||||||||||| ||||| ||||| ||||| || ||||| ||||  || ||  | |||||||||| ||  |
-atatgcctgcttgggtagttggatctatttcatttaacttttcttgtgat-ttaaagaaagagacacatatctaatcctgtttgatcaacactatatgcagGTTAATCCAAAAGCTGCTGAATCTTTGGCTGATCCTGAAGAGTATCCTAATTTATTTGAGGACTGGCAAGTTGGTCTTGCCATTGAATCTAAAGTTGCCG

upper sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
ggtaggagcatcagttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtac-atatattttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
  |   |  |      |      |        |    || |      | |   |   ||     || || | |  | |  | |  || |  |   |||||||| |    ||||||||| ||||||||||| ||||||||||| || || ||||||||||| || ||||||||||| || |   | |||||||||  |   |
catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttg-actgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG

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|7145778|gb|AW507700.1|AW507700
EST:     CAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAG                         GTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAAT
genomic: CAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAGgtaatttctg ... tttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAAT
EST: gi|7795673|gb|AW781070.1|AW781070
EST:     CAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAG                         GTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAAT
genomic: CAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAGgtaatttctg ... tttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAAT
EST: gi|16347999|gb|BI973594.1|BI973594
EST:     CAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAG                         GTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAAT
genomic: CAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAGgtaatttctg ... tttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAAT
EST: gi|208109455|gb|GD905843.1|GD905843
EST:     AAGTAAGGTCTCAGAGATAGTGGCAAATTTGGAGAAAAGACCTCAATAAG                         GTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAAT
genomic: AAGTAAGGTCTCAGAGATAGTGGC-AATTTGGAGAAAAGACCTCAATAAGgtaatttctg ... tttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAAT
EST: gi|207771312|gb|GD746427.1|GD746427
EST:     CAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAG                         GTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAAT
genomic: CAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAGgtaatttctg ... tttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcatgttgacgagtggctcatggattaaagagagtacatatattttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
     tgttgac  putative branch site (score: 3)
                                            ttttatt  putative PPT
                                  agtacatatattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaggagcatcagttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtacatatattttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - cattcat
- - - - - - - - - - - - - tgccttg
- - - - - - - - - - - - - - - - - - - - - - - - - tgttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggat