Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgtatgaatgattcttgatttattctatagtcattcctttttaactgttttcttctcttcctttcctatggcttatacttttcttttggttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGGAACCACTGCCCCTGGCCTACCCTATGTTGAACAAACTATAACCAATGCT

Basic information

species Glycine max
transcript GLYMA20G28980.1
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