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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatgctgcatttaaagttaagcatacagacattattcctgtagtgttgcgaaggataagtgttttgtatagttcattatgtttgattccttgtgtacagTTATCAGGCATTCCGTGCATATGGACAGTCAAAGCTTGCTAACATTTTACATGCCAATGAACTTGCTAGACGTCTTAAG

Basic information

species Glycine max
transcript GLYMA09G25070.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G25070.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
caatgctgcatttaaagttaagcatacagacattattcctgt-agtgttgcgaaggataagtgttttgtatagttcattatgtttgattccttgt-gtacagTTATCAGGCATTCCGTGCATATGGACAGTCAAAGCTTGCTAACATTTTACATGCCAATGAACTTGCTAGACGTCTTAAG
  ||||  | ||||   |  |   |       || | | ||| |   |     |    || |||  ||||    | ||   |||  ||    ||| |||||| ||  |  |  |  | |||||||| |||||||||||||| |||||||| ||||| ||||||||||||||  |  |||||
gtatgcaactttta---tgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaat-atatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG

upper sequence: GLYMA09G25070.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G009940_T02 (Zea mays), 3'ss of exon 4
------caatgctgcatttaaagttaagcatacagacattattcctgtagtgttgcgaaggataagtgttttgtatagttcattatgtttgattccttgtgtacagTTATCAGGCATTCCGTGCATATGGACAGTCAAAGCTTGCTAACATTTTACATGCCAATGAACTTGCTAGACGTCTTAAG
       | |||||   |   | |      ||| | |    || || |  | |   |||     ||    ||||  | |   || ||||           || ||| |||       |  |||||||||| || ||||||||||| ||||| || ||||| ||||||||||| || ||  || ||
gtatgtaattgctgtgctgtgattatgttctacggtctaatttactttgttttgaagaaaacctagccacttgttcaatc--ttgtgtt-----------gtgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG
















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|209720878|gb|BW662604.1|BW662604
EST:     TTCACCTATCGGGAAGGAATCCTTTTTGATAAACTTAATGATCAATCAAG                         TTATCAGGCATTCCGTGCATATGGACAGTCAAAGCTTGCTAACATTTTACA
genomic: TTCACCTATCGGGAAGGAATCCTTTTTGATAAACTTAATGATCAATCAAGgtaagaagta ... ttgtgtacagTTATCAGGCATTCCGTGCATATGGACAGTCAAAGCTTGCTAACATTTTACA
EST: gi|58022034|gb|CX708775.1|CX708775
EST:     TTCACCTATCGGGAAGGAATCCTTTTTGATAAACTTAATGATCAATCAAG                         TTATCAGGCATTCCGTGCATATGGACAGTCAAAGCTTGCTAACATTTTACA
genomic: TTCACCTATCGGGAAGGAATCCTTTTTGATAAACTTAATGATCAATCAAGgtaagaagta ... ttgtgtacagTTATCAGGCATTCCGTGCATATGGACAGTCAAAGCTTGCTAACATTTTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcgaaggataagtgttttgtatagttcattatgtttgattccttgtgtacagTTATCAGGCATTCCGTGCATATGGACAGTCAAAGCTTGCTAACATTTTACATGCCAATGAACTTGCTAGACGTCTTAAG
                                   gtttgat  putative branch site (score: 5)
                                         ttccttgt  CT-rich tract
                 ttttgtata  TA-rich tract