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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgcatctaatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggtttctgatttgtttggattggattgggttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG

Basic information

species Glycine max
transcript GLYMA20G35970.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G24100.1 (Arabidopsis thaliana), 3'ss of exon 4
----atttgcatc-taatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggtttctgatttgtttggattggattgggttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
    |||||| |  | ||   | || |||  || ||  | ||  ||   | |   |  || |     | | || |   ||| |||   |         |  ||||||| ||||| ||||| ||||| || || ||  | || ||||| |||||||| || |||||||| || |||||||||||||||
acatatttgcttggtgatgcatatcagtt-atatttg-tactgtgg---aacaaagaaatgcaataattgcttattggttggttgttcttctcatttcttaacagGGCTGATATCTGGTCATTTGGTATAACAGCACTTGAATTGGCCCATGGTCATGCACCTTTCTCAAAATATCCTCCCATGAAG

upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G10730.1 (Arabidopsis thaliana), 3'ss of exon 5
atttgcatctaatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggtttctgatttgtttggattggattgggttgg--acagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
  ||  || | |  |     |     |  |||     |   |  | |   |  || |       |||  || || |||||   |    |   ||    ||||||| ||||| ||||| ||||| || || ||| ||||||||||||| ||||| || |||||||| || ||||| || ||||||
--ttttatgtcaaatgaaatgaaaaatctttagaaactgtttgcatcaaagaaatgcaataacagttattggttggtttgttcttctgtaccttccttacagGGCTGATATATGGTCTTTTGGAATAACGGCGCTGGAGTTGGCTCACGGTCATGCACCTTTCTCAAAATATCCCCCTATGAAG

upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S227_24V6.1 (Physcomitrella patens), 3'ss of exon 4
atttgcatctaatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggttt-ctgatttgtttggattggattgggt----tggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
    |||  ||  |||  |     | |||   ||    |  | | | |||  || ||| |     | |  |||   |     |  ||  |  |     |   ||| || || || ||||| |||||||| ||||| |||||| | ||||||||||| || || |||||||||||||||||| |||||
----gcaatta-ctttgattcacatatacgacatttgactttctgcttgtacgagtctaaaaccctctgttgaccaggaataagcggtataagcattgtatgcagAGCTGACATCTGGTCCTTTGGGATAACTGCTTTGGAGCTTGCTCATGGTCATGCACCCTTCTCCAAGTATCCTCCCTTGAAG

upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S27_49V6.1 (Physcomitrella patens), 3'ss of exon 4
atttgcatctaatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggtttctgatttgtttggattg----gattgggttgg--acagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
      |  |  || || | |   |   |   |  | |  | | || ||| ||  |  || | |      |  || ||   ||         |  |||     |||||| || || ||||||||||||||||||||  ||||| | || |||||||| || || ||||| || |||||||| || |||
---aaaaaatggttctttttgagat-cgcaggagccgttagct-acttgt-tgtcttggattcgaaaagagggtttttataatcattaaagctccgttcattgcagGGCTGACATATGGTCGTTTGGGATTACTGCACTGGAGCTTGCACATGGTCATGCTCCATTCTCAAAATATCCTCCAATTAAG

upper sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ34917 (Selaginella moellendorffii), 3'ss of exon 4
atttgcatctaatttttgtcggtttgtacttaatgcttcggtttacctgtgtgattctgacttggtttctgatttgtttggattggattgg-gttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
                         ||| |  | |||||  ||| | | |    ||||  |   | |    |||| | |        |||  ||    |||||| ||||| ||||| || ||||| |||||||||||||||||||| || || || || || || || |||||||| ||||||
-------------------------gtaatgga-gcttcttttttcttcttc--ttcttgcc--gatgagaatttttctaagcgttgttgttgtcctgcagGGCTGATATCTGGTCCTTCGGGATCACTGCGTTGGAGTTGGCTCACGGGCATGCACCGTTTTCGAAATATCCTCCGATGAAG

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|6567234|gb|AW234845.1|AW234845
EST:     GATAGCGCCGGAGGTGCTGCAACCTGGAACCGGTTACAATTTCAA                         GGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCA
genomic: GATAGCGCCGGAGGTGCTGCAACCTGGAACCGGTTACAATTTCAAgtcagttagt ... ggttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCA
EST: gi|10845866|gb|BF068902.1|BF068902
EST:     GATAGCGCCGGAGGTGCTGCAACCTGGAACCGGTTACAATTTCAA                         GGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCA
genomic: GATAGCGCCGGAGGTGCTGCAACCTGGAACCGGTTACAATTTCAAgtcagttagt ... ggttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtgtgattctgacttggtttctgatttgtttggattggattgggttggacagGGCGGATATTTGGTCGTTTGGGATTACTGCGTTGGAGTTGGCTCATGGTCACGCGCCTTTCTCCAAGTATCCTCCCATGAAG
                          atttgttt  TA-rich tract