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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgtatgaatgattcttgatttattctatagtcattcctttttaactgttttcttctcttcctttcctatggcttatacttttcttttggttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGGAACCACTGCCCCTGGCCTACCCTATGTTGAACAAACTATAACCAATGCT

Basic information

species Glycine max
transcript GLYMA20G28980.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28980.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G149952_T01 (Zea mays), 3'ss of exon 1
-gttgtatgaatgattcttgatttattctatagtcattcctttttaactgttttcttctcttcctttcctatggcttatacttttcttttggttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGGAACCACTGCCCCTGGCCTACCCTATGTTGAACAAACTATAACCAATGCT
  ||  |||||||   ||     |    |  | | |         ||   |      |       ||   |   || ||  | ||   |   ||  | |||  ||||||| |||||||||  ||| |||||||||||||| || || ||||| || ||||| |||||  |||| ||||||||  |  | || |||||||||
cttttcatgaatgtgcctgagcatgcagttcattaagaggaagggaaagttacaacaccacaatcttagcaaacctaatgatctttcctctctt-ctgcagCATTGAGATCTATAAGCATAATAAGGAAGAAAGAATAGCACGGACATGGGGGACAACTGCACCTGGATTACCTTATGTTGAGGAGGCAATTACCAATGCT

upper sequence: GLYMA20G28980.2 (Glycine max), 3'ss of exon 1
lower sequence: AT5G43780.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------gttgtatgaatga--ttcttgatttattctatagtcattcc--tttttaactgttttcttctcttcctttcctatggcttatacttttcttttggttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGGAACCACTGCCCCTGGCCTACCCTATGTTGAACAAACTATAACCAATGCT
                  || |   | |||  |  |  | |   |  |||   |  |   ||| ||      |  |  |  |   | |  |||  |  |   ||   ||||  ||     || |||||||||| |||||||| ||||||||| |||| ||  |||| ||||||||||| || | ||| || || ||||  ||| || | || ||||| |||
gtaagtctctcttcctaattctgcaattgaaatcatcaaatgtatgcataagaaacctaatttgtagaaaaatcatcttgctttatactgatgattggttgattgaatttgaata-----gTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGGAACCACGGCTCGTGGGCTTCCTTATGCGGAAGAAGCAATCACCAAAGCT

upper sequence: GLYMA20G28980.2 (Glycine max), 3'ss of exon 1
lower sequence: AT4G14680.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------------------------------------------------------------gttgtatgaatgat-tcttgattt--attctatagtcattcctttttaactgttttcttctcttcct----ttcctatggcttatacttttcttttggttattt-cagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGGAACCACTGCCCCTGGCCTACCCTATGTTGAACAAACTATAACCAATGCT
                                                                                         ||  | |||| |  | |||||||  ||  |   || |||  | || |    |    ||  | |       |  ||        || | ||  | || || ||| |||| ||||||||||||| ||||| ||||||||  |||||||  |||||||||| || ||||| || ||  | || ||||| ||| |  | ||||||||||||
gtaagtttctcttaggttggattaggatttgaggaataaagttttcatttttatcgttctgttactgttgttgaggaataaagttttgatttgaggaataaagttttgatttttatagttctgttatttttgttgaggaatcagatttgcatagagagatcactgaatagagtaatgtttgtgtgtttgttttcagTATTGAGATTTATAAACATCCGAAAGAAGAGCGAATAGCGAGAACTTGGGGTACGACTGCACCGGGTTTGCCTTATGTAGAAGAGGCGATAACCAATGCT

upper sequence: GLYMA20G28980.2 (Glycine max), 3'ss of exon 1
lower sequence: AT3G22890.1 (Arabidopsis thaliana), 3'ss of exon 1
gttgtatgaatgattcttgatttattcta--tagtcattcctttttaactgttttcttctcttcctttccta-tggcttatacttttcttttggttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGGAACCACTGCCCCTGGCCTACCCTATGTTGAACAAACTATAACCAATGCT
     | || |     | || |   |||   || || |    ||  || |    | |     |  ||   || ||   | |  || | |||  |||   ||||| ||||||||||||||||||| || |||||||| |||||  |||| ||||| || || || || ||  | || || || ||  |  | ||||| ||||||
---tcacgattagacttagactagatctgattaatcttgagattagaatttggctatatgtgtaattggttactgaaatctgtttgtttttatgtttgatcagTATTGAGATTTATAAGCATCCAAAGGAAGAAAGGATAGCTAGAACATGGGGTACGACGGCTCCAGGTTTGCCTTACGTAGACGAGGCGATAACTAATGCT

upper sequence: GLYMA20G28980.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 1
-gttgta-tgaatgattcttgatttattctatagtcattcctttttaactgttttcttctcttcctttcctatggcttatacttttcttttggttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGGAACCACTGCCCCTGGCCTACCCTATGTTGAACAAACTATAACCAATGCT
    ||| |   |||    | || || | |    |  |||| ||  |||| |||       ||  |   |  |   | || | ||  ||| ||| |||||||| ||||||| || ||||| |  ||||||||||| |||||| |||||||||| || |||||||||||  | || ||||| || ||| | ||||||||| ||
ttgcgtactaggtgaagaataatgtaattttggattgttccattc-aactatttatggtgattgttcatcccttattgattcattgattt-ggtaatttcagTATTGAGATCTACAAGCACCACAAAGAAGAAAGGATAGCCAGAACTTGGGGGACTACTGCCCCTGGTTTGCCGTATGTGGATCAAGCAATAACCAATTCT

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|21888562|gb|BQ741775.1|BQ741775
EST:     AGGGTTGCTCCTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
genomic: AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
EST: gi|213598528|gb|DB958140.1|DB958140
EST:     AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
genomic: AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
EST: gi|254333225|gb|GR850475.1|GR850475
EST:     AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
genomic: AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
EST: gi|14990859|gb|BI316532.1|BI316532
EST:     AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
genomic: AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
EST: gi|254342980|gb|GR859142.1|GR859142
EST:     AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
genomic: AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
EST: gi|11412555|gb|BF424566.1|BF424566
EST:     AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
genomic: AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
EST: gi|17023313|gb|BM094347.1|BM094347
EST:     AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
genomic: AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
EST: gi|254323593|gb|GR840234.1|GR840234
EST:     AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
genomic: AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
EST: gi|4396339|gb|AI495336.1|AI495336
EST:     AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGNGG
genomic: AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
EST: gi|254316899|gb|GR828436.1|GR828436
EST:     AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
genomic: AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
EST: gi|208306002|gb|GE105747.1|GE105747
EST:     AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAA
genomic: AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAA
EST: gi|10709253|gb|BF008977.1|BF008977
EST:     TCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
genomic: TCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
EST: gi|254339556|gb|GR848273.1|GR848273
EST:     AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGA                         TGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG
genomic: AGGGTTGCTCTTTTCGATTCCAAGGGAGACCCTGTTGCAATTCTCAATGAgtaagacact ... gttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgttttcttctcttcctttcctatggcttatacttttcttttggttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGGAACCACTGCCCCTGGCCTACCCTATGTTGAACAAACTATAACCAATGCT
 ttttaac  putative branch site (score: 2)
                                  cttttcttttggtt  putative PPT
                             ttatacttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtatgaatgattcttgatttattctatagtcattcctttttaactgttttcttctcttcctttcctatggcttatacttttcttttggttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGGAACCACTGCCCCTGGCCTACCCTATGTTGAACAAACTATAACCAATGCT

- tgtatga
- - - - - - - - - - - - - - - - -cattcct