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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accgacacctttcatttctgactttgtttgggggatttcttcttgtatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG

Basic information

species Glycine max
transcript GLYMA13G42800.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 9
accgacacctttcatttctgactttgtttgggggatttcttcttgtat--gttataaatt-cttaaagcttcatctcatttcactaatgacttgttttgt-cagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
    ||   | |   |||||    || ||     | | | | |  |||  ||  || | | ||| ||   ||||   | | |  |  |   ||  ||| | ||||| ||||| || || |||||||||||||| |||||||||||||| |||||||| ||||||||||| |||
--aaacttttatatattctgcagctgattctaatactacgtatcatataagtggtatactgcttgaaatgtcatt--agtccgttgctccttttctttcttcagTTATGGGATATAAACATGGATTCAGGCCCAGTTGCAACTTTCCAAGTTCATGAATATTTAAGACCTAAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 9
accgacacctttcattt-ctgactttgtttgggggatttcttcttgtatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
   ||    |   |||| |||      |   || | | | ||  || | | | | | |||       ||    |||| | | |  |  | | || |  ||| | ||||| ||||| ||| | || || || |||||||| ||||||||||||||||||||||| ||||||
ggtgatttatactattttctgtagccatagaggtgttatttttctgca-gctgttacttcgatgtttttgtgttcatataaattttttccttttgttccagCTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 9
--------accgacacctttcatttctgactttgtttgggggatttcttcttgtatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
         |  |       ||| | |||||| |||     | |   || | |       ||||     | |  ||  | | | || | ||      | |||  |||| | |||||  | || ||||||||||| || ||| |||| ||||||||||||||  ||||||| ||||||
tttgcatggcttatgatgagcatatttgactt-gttaataaggtaaattttag------gtaaagcggaataatttggtttgagtttaatatctgtct-tttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 9
accgacacctttcatttctgactttgtttgggggatttcttcttgtatgttataaattcttaaa-gcttcatctcatttca-ctaatgact--tgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
        |||| |      |     ||| || | | |   ||| | || || | ||  |||   |||  |  | |||| |  |||    |  |||||   |||||||||||  | || |||||||||||||| ||||||||||| ||||||||||| || ||| | || |||
----tagactttgaggatcaaggaacttttggtgctctgcccttttgtgataaatatgtttatctgctagaaataattttagttaaccgtttttgtttctccagTTGTGGGATCTAAACATGGATTCAGGCCCAGTTGCAACTTTTCAGGTTCATGAATACTTACGTCCTAAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G51690.2 (Arabidopsis thaliana), 3'ss of exon 9
---------------accgacacctttcatttctgactttgtttgggggatttc--ttcttgtatgttataaattcttaaagcttcatctcatttcac-taatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
                    || | |||| |  |||  |    | |  | | ||  |   ||  |   ||   ||| |  |   | | || |   ||  | |||  ||   | | ||||| |||||||| || |||||  |||| || || |||||||||||||||||||| ||||| | ||| |||
gtccatattttcactgttttcatcattcaata-tgatatcccctcgaagttatcagtggctggtttcgatttgttcgtgtaaggtaaactgaccccatgttatgttttacat-gccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 9
accgacacctttcatttct--gactttgtttgggggatttcttcttgtatgtta---taaattcttaaagct-tcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
       | || |||  |   || ||  | ||    |||| |  || |   |||   ||    ||| ||    |||    | ||   |  | ||||| ||| |||||| ||||||||||||||||| |||||||| ||| |||| |||||||||||||| ||||||||||| |||
---aggtctttgcatcacaaggaattgatatgtactatttgtctttctggcttaagttagggccttgaactaatcactggaatttgtt--ttacttgcttt-tcagTTATGGGACATTAATATGGACTCAGGCCCAGTTTCAACCTTCCAGGTTCATGAATATTTAAGACCTAAG

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|7686354|gb|AW757002.1|AW757002
EST:     TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTCAGGCACCGTTGCAACTTTGCAGGTTCAT
genomic: TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAGgtttgaaatt ... gttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCAT
EST: gi|18730643|gb|BM525996.1|BM525996
EST:     TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCAT
genomic: TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAGgtttgaaatt ... gttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCAT
EST: gi|5770902|gb|AI974076.1|AI974076
EST:     TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCAT
genomic: TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAGgtttgaaatt ... gttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCAT
EST: gi|21887329|gb|BQ740542.1|BQ740542
EST:     TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACT
genomic: TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAGgtttgaaatt ... gttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACT
EST: gi|193711274|gb|FK646095.1|FK646095
EST:     TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAG                         TTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACCTTCCAGGTTCAT
genomic: TTGGGAAGGATGGTAGATACATACTTAGTCGTGATTACATGACTTTAAAGgtttgaaatt ... gttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttataaattcttaaagcttcatctcatttcactaatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG
                                 cactaat  putative branch site (score: 2)
                                          cttgtttt  putative PPT
     tataaattcttaaa  TA-rich tract