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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaactcaagattgatatcttgatttgtagttaagcagtaccaaagcatgcataggttcagtgtttagtctgttgtatagtagtgttatttttttaattcctttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTATTGTCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGTTTTTGG

Basic information

species Glycine max
transcript GLYMA14G14010.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G14010.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
gtaagtaactcaagattgatatcttgatttgtagttaagcagtaccaaagcatgcataggttcagtgtttagtctgttgtatagtagtgttatttttttaattcctttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTATTGTCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGTTTTTGG
|||| |  || || ||| |  | || |||   | | |    |  |    |  | ||    | ||     |||| || |   ||  | ||||| |  ||    || | | | |  ||  | |||||  | |||||||| || |||||| |||| || ||||| ||||| || ||| | || || || ||||||||||||||||| |||||||||||| |  | |
gtaatttcct-aatatttacctgttcattaaaattcatagggatcatttgatttcaaccatacaagcagtagtttgattgcta--aatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG

upper sequence: GLYMA14G14010.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G882708_T03 (Zea mays), 3'ss of exon 3
---------------------------gtaagtaactcaagattgatatcttg-----atttgtag-ttaagcagtaccaaagcatgc----ataggttcagtgtttagtctgttgtatagtagtgttatttttt----taattcctttttctgttgtttt---------cagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTATTGTCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGTTTTTGG
                               |  |||  | ||    ||||       ||||||   | ||  | |||  |   |||       | |   ||  || | ||        | || | | ||  ||     ||| || ||||||| || |  |         |||||| |||| ||||| || |||||| |||| || ||||| ||||| |||||  |||| || |||||||||||||||||||| ||||||||||| ||  | |
gtaaactttgcatgttaatttgtaattcctggggactagaaatgttcatctgaataacatttgtttctcaaaaactactgacatatgttcctgaaagcctagatttcaatcataaaagcaatactttgatagttaaaggtaactcatttttctcttatgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACAGTGCTGTCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGTTTTACTTG

upper sequence: GLYMA14G14010.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G882708_T01 (Zea mays), 3'ss of exon 1
gtaagtaactcaagattgatatcttgatttgtagttaagcagtaccaaagcatgcataggttcagtgtttagtctgttgtatagtagtgttatttttttaattcctttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTATTGTCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGTTTTTGG
                   ||     || |||   | |        |   ||  ||||    || |  || |   |||  |  |||   | |||||| |    | | |      ||  | |||||| |||| ||||| || |||||| |||| || ||||| ||||| |||||  |||| || |||||||||||||||||||| ||||||||||| ||  | |
-----------------actactgacatatgttcctgaaagcctagatttcaatcataaaagcaatactttgatagttaaa-ggtaac-tcatttttct----cttatgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACAGTGCTGTCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGTTTTACTTG

upper sequence: GLYMA14G14010.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------gtaagtaactc--aagattgatatcttgatttgtagttaagca-gtaccaaagcatgcataggttcagtgtt----tagtctgttgtatagtagtgttatttttttaattcctttttctgt-tgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTATTGTCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGTTTTTGG
                                                           || | |||||    | |||  | |||  |    || | |   | ||  || |      | |  |  |  ||      | |   |||    |||  | ||  |  ||  |  |||   |||  ||  | |||||| |||| ||||| || |||||| |||| || ||||| ||||| || ||| |||| || |||||||| ||||||||||| ||||||||||| ||  | |
gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttttgacatttgtttctcaaaaactactgatatatgtttcagaaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG

upper sequence: GLYMA14G14010.2 (Glycine max), 3'ss of exon 1
lower sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagtaactcaagattgatatcttgatttgtagttaagcagtaccaaagcatgcataggttcagtgtttagtctgttgtatagtagtgttatttttttaattcctttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTATTGTCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGTTTTTGG
    || | |     |||||||  |  || ||| |       |      || || |   || |  | || |  ||      | ||| || ||||| |||     || ||| || || |  |||||||| || |||||||| ||||| || ||||| || |||||||| || |||||||| || || || ||||| || ||||| ||||||||||| |||||||
----gtgaattttctttgatatgctcgtt-gtattgttttgatggtggtgcctgaaagtgtcctcttttaaacct------tggtattgatatttgtttg----ctgtttttgatgata-cagTATCTGTCCAATGCTGCTCTTGCTCGTACAAGTGTGGCAAGTACTACTGTATTGTCTTCAACCTCGGGACTGTTTACTCTGTTCATTGGTGTATTTTTGG

upper sequence: GLYMA14G14010.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtaactcaagattgatatcttgatttgtagttaagcagtaccaaagcatgcataggttcagtgtttagtctgttgtatagtagtgttatttttttaattcctttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTATTGTCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGTTTTTGG
                   | ||||  || |   ||      ||| |  | | |   ||||| |  ||    | ||  | |    || |  | |  || | |    |||||| || ||| |||||| | ||||||||||| |||||||| ||||| ||||| |||||||| ||  | || || |||||||||||||||||||| ||||||||||   ||||||
-------------------tgtctt--ttagggattctattttacaatggta-gtccaggttaaa-gtcctatgtgaaggaattcagagagagtacttgattgtgattttctattttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG

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|254326132|gb|GR840724.1|GR840724
EST:     AAATTGCTACTTATGGATTTTACATTGCACCTATCTGGTTTATAACTGAG                         TATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTA
genomic: AAATTGCTACTTATGGATTTTACATTGCACCTATCTGGTTTATAACTGAGgtaagtaact ... ttgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTA
EST: gi|21888005|gb|BQ741218.1|BQ741218
EST:     AAATTGCTACTTATGGATTTTACATTGCACCTATCTGGTTTATAACTGAG                         TATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTA
genomic: AAATTGCTACTTATGGATTTTACATTGCACCTATCTGGTTTATAACTGAGgtaagtaact ... ttgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTA
EST: gi|192325901|gb|FK016578.1|FK016578
EST:     AAATTGCTACTTATGGATTTTACATTGCACCTATCTGGTTTATAACTGAG                         TATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTA
genomic: AAATTGCTACTTATGGATTTTACATTGCACCTATCTGGTTTATAACTGAGgtaagtaact ... ttgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtctgttgtatagtagtgttatttttttaattcctttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTATTGTCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGTTTTTGG
                           ttttaat  putative branch site (score: 3)
                        tttttttaattccttt  CT-rich tract
        ttgtatagtagtgtta  TA-rich tract