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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttgaaaaattaagcatgaaagcacgattcctgttcctgtagtatttatcgactggagaagtgttatgtacaattacatttgcttccttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACATGCAAATGAACTTACAAGACGTCTCAAG

Basic information

species Glycine max
transcript GLYMA20G30080.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30080.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
tttcttgaaaaattaagcatgaaagcac---gattcctgttcctgtagtatttatcgactggagaagtgttatgtacaattacat---ttgcttccttgat-ttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACATGCAAATGAACTTACAAGACGTCTCAAG
           ||  | | |  | ||||   | ||    || |  |  ||  |  |  |    ||| |||  ||||| | || ||   |   |    || | | ||| ||||||  |    | ||||||||||||||||||||||| |||||||| ||||| ||||||||| | ||  |  | |||
---------gtatgcaacttttatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatatatggttcaatcttgtgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG

upper sequence: GLYMA20G30080.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G009940_T02 (Zea mays), 3'ss of exon 4
tttcttgaaaaattaagcatgaaagcacgattcctgttcctgtagtatttatcgactggagaagtgttatgtacaattacatttgcttccttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACATGCAAATGAACTTACAAGACGTCTCAAG
  | |  ||    |  || ||  |  | | |    | ||   |    ||| |    || ||||    ||   ||   | || |   |   |||  | ||| || |  | |    ||||||||||||| ||||||||||| ||||| || ||||| ||||||||| | || ||  |  ||
-gtatgtaattgctgtgc-tgtgattatgttctacggtctaatttactttgtt--ttgaagaaaacctagccacttgttcaatc-ttgtgttg--tgcagGTATAGTAGCATTGGTGCATATGGGCAATCAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG
















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|151394515|gb|EV264386.1|EV264386
EST:     TTTGCATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAG                         TTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
genomic: TTTGCATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAGgtaatatgta ... ttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
EST: gi|151398063|gb|EV267941.1|EV267941
EST:     TTTGCATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAG                         TTACGACAACTGGCGTGCATATGGGCAGTCAAAGCTT
genomic: TTTGCATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAGgtaatatgta ... ttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTT
EST: gi|19452661|gb|BM954071.1|BM954071
EST:     TTTGCATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAG                         TTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
genomic: TTTGCATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAGgtaatatgta ... ttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
EST: gi|209715120|gb|BW677163.1|BW677163
EST:     TTTGCATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAG                         TTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
genomic: TTTGCATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAGgtaatatgta ... ttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
EST: gi|14205703|gb|BG839381.1|BG839381
EST:     TTTGCATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAG                         TTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
genomic: TTTGCATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAGgtaatatgta ... ttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
EST: gi|31473948|gb|CD415976.1|CD415976
EST:     GAATCTGTTTTGACAAAATTAATGATGAATCAAG                         TTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
genomic: GAATCTGTTTTGACAAAATTAATGATGAATCAAGgtaatatgta ... ttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
EST: gi|26269039|gb|CA820102.1|CA820102
EST:     TTTGCATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAG                         TTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
genomic: TTTGCATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAGgtaatatgta ... ttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
EST: gi|14206074|gb|BG839752.1|BG839752
EST:     CATATTCTGAAGGAATCTGTTTTGACAAAATTAATGGTGAATCAAG                         TTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTAAC
genomic: CATATTCTGAAGGAATCTGTTTTGACAAAATTAATGATGAATCAAGgtaatatgta ... ttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTT-AC
EST: gi|22930059|gb|BU547198.1|BU547198
EST:     CTGTTTTGACAAAATTAATGATGAATCAAG                         TTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
genomic: CTGTTTTGACAAAATTAATGATGAATCAAGgtaatatgta ... ttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
EST: gi|31471558|gb|CD413586.1|CD413586
EST:     ATGATGAATCAAG                         TTACAACAACTGGCGTGCATATGGCCAGTCAAAGCTTGCCAACATTTTACA
genomic: ATGATGAATCAAGgtaatatgta ... ttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
EST: gi|192319094|gb|FK010630.1|FK010630
EST:     TTTGACAAAATTAATGATGAATCAAG                         TTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA
genomic: TTTGACAAAATTAATGATGAATCAAGgtaatatgta ... ttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttatcgactggagaagtgttatgtacaattacatttgcttccttgatttcagTTACAACAACTGGCGTGCATATGGGCAGTCAAAGCTTGCCAACATTTTACATGCAAATGAACTTACAAGACGTCTCAAG
                                           ccttgat  putative branch site (score: 5)
                                    tttgcttcctt  CT-rich tract
                             aattacattt  TA-rich tract