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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

cgtaagtttctggtattttgaagttaattaatctgtgttgtattttgtggctgttataaaatagttactaattatttttttcactgtgttcccaaatgactgtataGGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCCACCCGAGTGATGGGTACATATGGTTAT

Basic information

species Glycine max
transcript GLYMA18G45200.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 4
---------cgtaagtttctggtattttgaagttaattaatctgtgttgtat---tttgtggctgttataaaatagttactaattatttttttcactgtgttcccaaatgactgtataGGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCCACCCGAGTGATGGGTACATATGGTTAT-
         | |   || |   ||| |||   ||  ||  | | | || |||   | ||| |    |||  ||   ||  | || ||    || |   | |      |    |  | |||| ||||| || ||||| ||||| ||||| || || ||||| || ||| |||| ||| ||||||||||||| || || |||||||| |||||||||||| 
gttgagtagcatttcttgccaatatcttgtttttt-ttcctttctcttctatgcatctgttgggaatatgtaaatatttttcataatagcatttatcttttatttgcac--ttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACTCGGGTGATGGGAACATATGGTTATG

upper sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 3'ss of exon 4
---------cgtaagtttctggtattttgaagttaattaa-tctgtgttgtattttgtggctgttataaaatagttactaattatttttttcactgtgttcccaaatgactgtataGGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCCACCCGAGTGATGGGTACATATGGTTAT-
         | |   ||     | | |||   ||  ||   | | | || |||  ||| |    |||  ||   ||  | || ||    || |   | |    | |    |  | |||| ||||| || ||||| ||||| ||||| || || ||||| || ||| |||| ||| ||||||||||||| || || |||||||| |||||||||||| 
gttgagtagcatttcttgtcaatgtcttgttttttttttcctttctcttctatgctgttgggaatatgtaaatatttttcataataacatttatcttttatttacac--ttacacagGATTATACTGCTAAACTCTCTGACTTTGGTCTGGCAAAAGCTGGCCCAGAAGGCGATCAAACCCATGTATCAACACGGGTGATGGGAACATATGGTTATG

upper sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G01020.1 (Arabidopsis thaliana), 3'ss of exon 3
cgtaagtttctggtattttgaagttaattaatctgtgttgtattttgtggctgttataaaatagttactaat--tatttttttcactgtgttcccaaatgactgtataGGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCCACCCGAGTGATGGGTACATATGGTTAT-
 |||||    |  | ||||     |  ||   |   ||||      |    ||  |  |  |    || | |  ||| |  || | || | |     ||||   |  ||||||| || ||||| ||||| ||||||||  |||||||||| ||||| || |||||||||||||||||||| || ||||| |||||||| ||||| ||| 
-gtaagcagttattcttttctttctgctttgccaaagttgctccaagatattgggaatacctttccacaactaatatatccttgattgggct----gatgaaccttcagGACTACACCGCCAAGCTTTCAGATTTTGGCTTAGCTAAAGCTGGACCCCAGGGTGATGAAACCCATGTATCAACTCGAGTTATGGGTACTTATGGCTATG

upper sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 4
cgtaagtttctggtattttgaagtta-attaatctgtg---ttgtattttgtggctgttataaaatagttactaattatttttttcactg-tgttcccaaatgactgtataGGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCCACCCGAGTGATGGGTACATATGGTTAT-
 ||||||  |   | | || ||   | ||||  |       || | | |  | ||  | ||   | | |   | | |  | ||| | ||| |  || |   ||| | || |||| ||||||||||| |||||||| ||||| || || ||||| ||||||||||||||||| ||||||||||| || || || |||||||| ||||||||| 
-gtaagtagc--atttcttaaaaccacattagccaagacatttttttctcattgccatcatgggagaatgcttcactcctgtttaccctgctaatcaccggtgaatctacagGATTATACAGCCAAGCTTTCTGACTTTGGGCTTGCAAAAGCTGGACCACAAGGTGATGAGACCCATGTATCAACTCGTGTAATGGGTACCTATGGTTATG

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|208054421|gb|GD851856.1|GD851856
EST:     AGGCCTGTAATCTATCGTGACTTCAAAACGTCTAATATATTATTGGACTC                         CGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACA
genomic: AGGCCTGTAATCTATCGTGACTTCAAAACGTCTAATATATTATTGGACTCcgtaagtttc ... tgactgtataGGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACA
EST: gi|208187283|gb|GD982177.1|GD982177
EST:     AGGCCTGTAATCTATCGTGACTTCAAAACGTCTAATATATTATTGGACTC                         CGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACA
genomic: AGGCCTGTAATCTATCGTGACTTCAAAACGTCTAATATATTATTGGACTCcgtaagtttc ... tgactgtataGGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACA
EST: gi|193339928|gb|FK306619.1|FK306619
EST:     AGGCCTGTAATCTATCGTGACTTCAAAACGTCTAATATATTATTGGACTC                         CGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACA
genomic: AGGCCTGTAATCTATCGTGACTTCAAAACGTCTAATATATTATTGGACTCcgtaagtttc ... tgactgtataGGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttataaaatagttactaattatttttttcactgtgttcccaaatgactgtataGGACTATACAGCCAAACTTTCTGATTTTGGACTAGCTAAAGCAGGACCACAAGGTGATGAAACCCATGTATCCACCCGAGTGATGGGTACATATGGTTAT
              tactaat  putative branch site (score: 1)
     taaaatagttactaat  TA-rich tract