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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaaaattattacctttctcatacccacaactagtgtgcacatttatggttttttagtgtttcactacagttttcatactaacatatgtaatttttagGTAGCTTGCGGTGGAAATGGTGCAACTACTGTTTCTGCAACAATGCTTTTTGCTTCAATG

Basic information

species Glycine max
transcript GLYMA09G00500.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G00500.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0009g02380.t01 (Vitis vinifera), 3'ss of exon 4
-aaaaaaaattattacctttctcatacccacaactagtgtgcacatttatggttttttagtgt--ttcactacagttttcatactaacatatgtaatttttagGTAGCTTGCGGTGGAAATGGTGCAACTACTGTTTCTGCAACAATGCTTTTTGCTTCAATG
 |       ||| ||     ||  |        |||   |   ||| ||| | |||| | | |  || | |    | |  || || |  |||||   | |||||| |||  | | || |||||||||||||||||||||||||| ||| ||||||||||||||
catttctttttaatatgaagcttctcaattaggctaaaattgccatctattgcttttcattttccttgattgtgttctatatgctgatttatgt---tcttagGTGGCTACCAGAGGGAATGGTGCAACTACTGTTTCTGCAACCATGTTTTTTGCTTCAATG

upper sequence: GLYMA09G00500.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ25993 (Selaginella moellendorffii), 3'ss of exon 1
aaaaaaaattattacctttctcatacccacaactagtgtgcacatttatggttttttagtgtttcactacagttttcatactaacatatgtaatttttagGTAGCTTGCGGTGGAAATGGTGCAACTACTGTTTCTGCAACAATGCTTTTTGCTTCAATG----------------------------------------
                                                  ||    |  | |||| ||    | | || | | |    | |  |    || | ||| | || ||||| || ||||| |||||||| ||||||||| |||||||||||| |                                        
--------------------------------------------------gtaagctcttttttctct-tgttctccacagttagtgtttttctacgcagCTCGCTCGTGGAGGAAACGGAGCAACCACTGTTTCAGCAACAATGTTTTTTGCTTCAAAGGTAGTTTCTACATTGGAAAAAAGAGGAGCCTTTGGGGAAT
















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|18734973|gb|BM528493.1|BM528493
EST:     TTTTGGGAACCAGAGCTCAGAAGACAGCTCGAAGGGACATCGCACATGTT                         GTAGCTTGCGGTGGAAATGGTGCAACTACTGTTTCTGCAACAATGCTTTTT
genomic: TTTTGGGAACCAGAGCTCAGAAGACAGCTCGAAGGGACATCGCACATGTTgtgagtgttt ... taatttttagGTAGCTTGCGGTGGAAATGGTGCAACTACTGTTTCTGCAACAATGCTTTTT
EST: gi|298172196|gb|HO021788.1|HO021788
EST:     TTTTGGGAACCAGAGCTCAGAAGACAGCTCGAAGGGACATCGCACATGTT                         GTAGCTTGCGGTGGAAATGGTGCAACTACTGTTTCTGCAACAATGCTTTTT
genomic: TTTTGGGAACCAGAGCTCAGAAGACAGCTCGAAGGGACATCGCACATGTTgtgagtgttt ... taatttttagGTAGCTTGCGGTGGAAATGGTGCAACTACTGTTTCTGCAACAATGCTTTTT
EST: gi|298176891|gb|HO026898.1|HO026898
EST:     TTTTGGGAACCAGAGCTCAGAAGACAGCTCGAAGGGACATCGCACATGTT                         GTAGCTTGCGGTGGAAATGGTGCAACTACTGTTTCTGCAACAATGCTTTTT
genomic: TTTTGGGAACCAGAGCTCAGAAGACAGCTCGAAGGGACATCGCACATGTTgtgagtgttt ... taatttttagGTAGCTTGCGGTGGAAATGGTGCAACTACTGTTTCTGCAACAATGCTTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatggttttttagtgtttcactacagttttcatactaacatatgtaatttttagGTAGCTTGCGGTGGAAATGGTGCAACTACTGTTTCTGCAACAATGCTTTTTGCTTCAATG
                                 tactaac  putative branch site (score: 0)
                                                ttttt  putative PPT
                           ttttcatactaacata  TA-rich tract