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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctcttttctgttgtagcacaaaacaattagtatcatgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

Basic information

species Glycine max
transcript GLYMA16G01680.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 2
----------------gtaagttctcttttctgttgta-gcacaaaacaattagt------atcatgagttaacccatatt--acaatttaata----tttctgcac----gatttgcta--cttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
                 ||  || | |  | | || || |||      |    ||      || |||| |      |||||  |  |||| | |    || |  |||     ||||  ||   ||||||||||||||| |||  ||||||||| |||||||||||  ||||
gtaagttaatatgatcatattttttttactttattatatgcaaggtttatcccgtgatcagattatgattacttttatatttaatgatttgaaacaatttccatcacttttaatttattatgtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG

upper sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G116919_T01 (Zea mays), 3'ss of exon 5
--------gtaagttctc---ttttctgttgtagcacaaaacaattagtatcatgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
        | || | |        |   ||| | |    | | | |  |    |||| || | | |       |  ||||   ||      ||   | |||||||||||||||| |||  ||||||||| |||||||||||  ||||
ccaccccggcaaatgcggagaggctgctttgaacctgggacctagtgattcagtgagatagctctt-------tgaaataacgctcattatttcattgcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG

upper sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G116919_T02 (Zea mays), 3'ss of exon 5
--------gtaagttctc---ttttctgttgtagcacaaaacaattagtatcatgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG------------------------------------------------------------
        | || | |        |   ||| | |    | | | |  |    |||| || | | |       |  ||||   ||      ||   | |||||||||||||||| |||  ||||||||| |||||||||||  ||||                                                            
ccaccccggcaaatgcggagaggctgctttgaacctgggacctagtgattcagtgagatagctctt-------tgaaataacgctcattatttcattgcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAGGTACACATATACCAATAACTAGCTTATTACATGAACAGTAATGTTTTTTTGGAAGACATA

upper sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G177276_T01 (Zea mays), 3'ss of exon 5
gtaagttctcttttctgttgtagcacaaaacaattagtatcatgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
|||||||||    |   |||| |   | |     |  | | || | |    |   | ||    | | ||||     || || |      |||||||||||||| |||  ||||||||| |||||||||||  ||||
gtaagttctgaacttgcttgtggattatagatgcttttgttattattagctctgaaataatgctcattatt-----acaatgt------tttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG

upper sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G17280.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttctcttttctgttgtagcacaaaacaattagtatcatgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
|||||  |  | | |  ||   |  ||    | || ||||||    |||||   | | | |    ||||  |   || |        | ||| |||||||||||||||| |||||||| |||||||||||||||||
gtaaggacaatctgcactttctgttca--ttatttcgtatca---attaacttgtctaatatcgaaataagttgacatgg-------catttacagTTCATCCAGAAAGCTGGAATCCGATGTGGTCTGTATCAAG

upper sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G50430.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttctcttttctgttgtagcacaaaaca-attagtatca-tgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
|||||  |  | |||  ||  |   |       |||| | ||| |||  |   |  |  |  ||||   | | ||    |   |   | | | | |||||||||||||||| |||||||| |||||||| || |||||
gtaagcacagtcttcattttcattcctttgtttattaatttcaatgaacttgtctgttatctaattagctttatcattcca--tcattccatgtacagTTCATCCAGAAAGCTGGAATCCAATGTGGTCAGTGTCAAG

upper sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g00280.t01 (Vitis vinifera), 3'ss of exon 7
gtaagttctcttttctgttgtagcacaaaacaattagtatcatgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
||||||    |  | | |  ||| |   || |     | | ||   |  |   | |     |||| || ||         | || ||||||| |||||||||||||||| ||||| || |||||||||||||||||
gtaagtctcttgctgtttcatag-atggaaaatcctttcttatttat--atttagaagttgattttattttcacttttattctgttacttttccagTTCATCCAGAAAGCTGGAACCCAATGTGGTCTGTATCAAG

upper sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S366_17V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------------------------------------------------------gtaagttctcttttctgttgtagcacaaaacaattagtatcatgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
                                                                                                         || | |||  || | |     ||      |  | || |     ||   |    | |  |  | | ||  |      |||         || ||||||||||||| | ||||||||| ||||||||||| |||||
gtacgtactcgtgccgttatttccttgtatttcagtttgcactgcttctggtctgtgagtagctcattttcaggataagtccactgcaaatattttttcttgttgaattcctcccttttatccctacatgtggaatgttgtgtttctggtgccctggaaatgta-ctgagtacatgaaatggatcgaaatgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG

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|192307581|gb|FG999620.1|FG999620
EST:     ACGGTTCATGACACAGAAAAAGATCTGTTTGTCTATGAGTGACT                         TTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
genomic: ACGGTTCATGACACAGAAAAAGATCTGTTTGTCTATGAGTGACTgtaagttctc ... acttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
EST: gi|15661834|gb|BI699205.1|BI699205
EST:     TAATGGACGGTTCATGACACAGAAAAAGATCTGTTTGTCTATGAGTGACT                         TTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
genomic: TAATGGACGGTTCATGACACAGAAAAAGATCTGTTTGTCTATGAGTGACTgtaagttctc ... acttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG
                                           ctactttt  CT-rich tract
            atattacaatttaata  TA-rich tract