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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgttcatgtcttgaaagaaggttttgcctttttttttcagtcttgtaagttgaaagcaatctgacaaatttctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG

Basic information

species Glycine max
transcript GLYMA02G35500.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 4
--gcatgttcatgtcttgaaagaaggttttgcctttttttttcagtct---tgtaagttgaaag-caatctgacaa----------atttctatttt--------tagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG
     |  |||| | |||           |||  | ||| |  | |||   ||| |     ||| |||  |  ||           |||  |||  |        |||||||| |||||||| |||||||||||||||| ||| ||||| || |||||||| |||||| | || |||
gtaagtactcatattttgggttgctaaaatgctatctttctataatctagatgtgatacacaagtcaacttttcactgttttgatcattcatatgctgtgaaacatagGTTCTCAGCAACACAATTAAGCAAAAGAGGATGGAAAAGGCTGGCAAATGGGAGGTTCCTTTGCCAAAG

upper sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G009876_T01 (Zea mays), 3'ss of exon 4
gcatgttcatgtcttgaaagaaggttttgcct-ttttttttcagtcttgtaagttgaaagcaatc--tgacaaatttctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG
|    ||  |||  |         |   ||   || |  | ||||   ||    ||  |   |||  ||| |  |    |  | |||||||| |||||||| || ||||||||||||||||| ||||| || ||||||||||||||||| || |||
gtgaattactgttcttggcttctctccagctaattatgatacagtaacgttttatggcattgatcactgatatctggtgaagtgtagGTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG

upper sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 4
gcatgttcatgtcttgaaagaaggttttgccttttttt----------ttcagtcttgtaag--ttgaaagcaatc-tgacaaatttctatt----tttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG
  |   | | || || |   || |        |||             |    |   ||||   || |  ||| |  | ||  ||||||  |      ||||| || |||||||| || ||||||||||||||||| ||||| || |||||||||||||| || || |||
-tacagtaacgttttaagtcaaagcaacataatttggaacagagggggtatgatacagtaacgttttatggcattgatcactgatttctggtgaagcgtagGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG

upper sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 4
----gcatgttcatgtcttgaaagaaggttttgcctttttttttcagtcttgtaagttgaaagcaatctgacaaatttctattttt------agGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG
    |  ||||  |   ||  |||  |   |  |  |  || |  |   | || |   |  |  |   | |||| | | | |||||      |||||||||||||||||||||| ||||||||||| ||||| || || |||||||| || ||||| || |||
gtttgtttgttttttcttttcaagttgagatatctataattctgtaacttggtga--cggcattacattaacaagtgtgtgtttttgggtgtagGTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG

upper sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 4
-------gcatgttcatgtcttgaaagaaggttttgcctttttttttcagtcttgtaagttgaaagcaatctgacaaatttctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG
       || |||| ||||  | |     |  |      |  | |      | ||    |||      ||||||||   |||| | | |||||||||||||| || || |||||||| ||||| ||||| || ||||||||||| || |||||||| || 
gtctattgc-tgttgatgtacttattatcgaatacaaactcatgtacattacatgctctttgtgg---atctgacattattctgtctatagGTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAA

upper sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S136_220V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------gcatgttcatgtcttgaaagaaggt-tttgcctttt---tttttcagtcttgtaagttgaaagcaatctgacaa-atttctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG
              | ||||| |   |    ||    |||||| |     |   |   | | |||  ||      |   |      ||    ||||| ||||||| ||||||||||| ||||| ||  | ||||||||||| || |||||||| || ||||| ||||||
gtactcctgaaagtttttcattttgcggtgaaaaacatttgccgtcaaagtcacttcatttcgtattttccgcctataatactttcatgcgaattttcagGTTCTCAGCAACACCATCAAGCAGAAACGTAAGGAGAAGGCTGGTAAATGGGAGGTGCCTCTTCCTAAG

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|192313831|gb|FK007647.1|FK007647
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAA--GAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|15203872|gb|BI426640.1|BI426640
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|4307640|gb|AI444076.1|AI444076
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCA
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCA
EST: gi|7478670|gb|AW666357.1|AW666357
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|6071298|gb|AW100685.1|AW100685
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|23733288|gb|BU764826.1|BU764826
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|17519530|gb|BM188572.1|BM188572
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|298194398|gb|HO041046.1|HO041046
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|15203893|gb|BI426661.1|BI426661
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|8285802|gb|BE023361.1|BE023361
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|120491259|gb|EH219426.1|EH219426
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|192328211|gb|FK020444.1|FK020444
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|21995126|gb|BQ786654.1|BQ786654
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|192313774|gb|FK007646.1|FK007646
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAA--GAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|20811431|gb|BQ295909.1|BQ295909
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|7588724|gb|AW704513.1|AW704513
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|151402809|gb|EV272622.1|EV272622
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
EST: gi|6668126|gb|AW279577.1|AW279577
EST:     GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAG                         GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG
genomic: GAGCTGTTCCTGCATATCTTCTTGATCGTGATAACACGACCAGAGCAAAGgcatgttcat ... ctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttttttttcagtcttgtaagttgaaagcaatctgacaaatttctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG
                                atctgac  putative branch site (score: 3)
                                          tttctattttt  putative PPT
                                     acaaatttctattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgttcatgtcttgaaagaaggttttgcctttttttttcagtcttgtaagttgaaagcaatctgacaaatttctatttttagGTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA