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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactcttgttggcatattgcatggaaagaaactcctctgtttaatgtgttgattgcacatttgaagttgaaagaaataatattctttctttcctttgaagTAACAATGCAGGGGTGATGGCAACTCCATTCACGCTTTCCCAAGACAATATTGAATTGCAGTTCGCAACCAATCATTTAG

Basic information

species Glycine max
transcript GLYMA08G01870.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G01870.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 1
---aactcttgt-tggcata-ttgcatggaaagaaactcctctgtttaatgtgttgattgcacatttgaagttgaaagaaataatattctttctttcctttgaagTAACAATGCAGGGGTGATGGCAACTCCATTCACGCTTTCCCAAGACAATATTGAATTGCAGTTCGCAACCAATCATTTAG
   |     ||| |  |||  |||  |||      | |  |  |  |  |   || || || |||   |  |    |    |     |  |  |||  |||| || |||||||||||||||||||||||||| ||| | || ||  | ||   ||| || ||||| || || || || ||| | |
acaagtgtctgtgtttcatgcttgtttggttgcgtagttattagaatgcttcttttatagctcatcacacttcctgattggt-----tggtggttttgtttgcagCAACAATGCAGGGGTGATGGCAACTCCTTTCTCTCTCTCAAAGGATGGTATCGAGTTGCAATTTGCCACTAACCATGTTG

upper sequence: GLYMA08G01870.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0025g03380.t01 (Vitis vinifera), 3'ss of exon 2
aactcttgttggcatattgcatggaaagaaactcctctgtttaatgtgttgattgcacatttgaagttgaaagaaata-atattctttctttcctttgaagTAACAATGCAGGGGTGATGGCAACTCCATTCACGCTTTCCCAAGACAATATTGAATTGCAGTTCGCAACCAATCATTTAG
  ||      ||| | ||   |  | |    | |     |    | || |  |    | ||||||  |  | |||  | ||  ||||| |||  || ||||||||||||||||||| ||||| |||||||||  ||||||||| ||||| || ||  ||||||| |||||||| |||||||
ccctaccacaggctttttctctt-acacttgcacacacatagcttctgctcctctttcttttgaaaattcaggaatgacattgtctttttttatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACATAGAGCTGCAGTTTGCAACCAACCATTTAG
















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|208336865|gb|GE135549.1|GE135549
EST:     AAATTTTCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGG
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGG
EST: gi|13789180|gb|BG651771.1|BG651771
EST:     AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGATGGCAACTCCATTCACGCTTTCCCAAGACAATAT
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGGCAACTCCATTCACGCTTTCCCAAGACAATAT
EST: gi|208096538|gb|GD893309.1|GD893309
EST:     AAATTTTCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGCGATGG
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGG
EST: gi|208273474|gb|GE066770.1|GE066770
EST:     CAGCAGATTTTAATTTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGTGGATGGCAACTCCATTCACGCTTTCCCAAGACAATA
genomic: CAGCAGATTTTAA-TTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGT-GATGGCAACTCCATTCACGCTTTCCCAAGACAATA
EST: gi|208320039|gb|GE116384.1|GE116384
EST:     AAATTTTCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAAT                         TAACAATGCAGGGGCGATGG
genomic: AAATTTGCAGCAGATTTTAATTCTTCTGGTCTTCCACTCAATATCCTAATgtaagaactt ... tcctttgaagTAACAATGCAGGGGTGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttgattgcacatttgaagttgaaagaaataatattctttctttcctttgaagTAACAATGCAGGGGTGATGGCAACTCCATTCACGCTTTCCCAAGACAATATTGAATTGCAGTTCGCAACCAATCATTTAG
 tgttgat  putative branch site (score: 4)
                                  tattctttctttcctt  putative PPT
                        aaagaaataatattct  TA-rich tract