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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgctgattaaaatcttggctaccaataaactttcacctcatttgttatgatacgttatggcaagtttgttggtactttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC

Basic information

species Glycine max
transcript GLYMA08G20640.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g37160.1 (Oryza sativa), 3'ss of exon 6
---gtattgctgattaaaatcttggctaccaataaact-ttcacctcatttgttatgatacgttatggcaagtttgttggtactttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC
   |   | |    | ||  ||   ||    || ||||  |     |  | | | ||||   ||      | ||     | ||| || ||||  ||||| |||| ||||||||| || |||||    |||||| |    | ||||   |||||||| |||||||| ||||||||||| ||||||||||| |
gtagagcttccttctgaagact---cttttgatgaactacttgttcccctcgatttgatttatt----tgaatt-----gaactgttgcagGCTAGTGAGATCATATGGGCATCTCGTTGGGATGTCTATCTTCTTTCAAGTGATAGCCAGATCCATTGGTTCTCAATCATTAACTCACTGATGATTGTCC

upper sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G55130.1 (Arabidopsis thaliana), 3'ss of exon 6
gtattgctgattaaaatcttggctaccaataaactttcacctcatttgttatga-tacgttatggcaagtttgttggtactttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC
       | | |||    ||  || |     |||| |    | ||  | | | |  |  |||||  |||| ||     |  | | ||||| |||| |||||||||||| || || |||||||||||  |  | ||||| |||||||| ||||||||||| || ||||| ||||| || |||||||| |
------gtaactaa----tttact-ctggagaactctttatttatgcgctgtaaacatattatg--aagtatg-----aaatatgcagGAGAGTGTTATCAAATGGGCTTCGCGCTGGGACACATACTTGCTTATGAACGATGATCAAATCCACTGGTTTTCAATCATAAACTCGCTTATGATTGTCC

upper sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G13772.1 (Arabidopsis thaliana), 3'ss of exon 6
gtattgctgattaaaatcttggctaccaataaactttcacctcatttgttatgatacgttatggcaagtttgttggtactttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC
   |   ||| | | |  | | || |   |     || || |  |  |||   | || || |    | |||| || |       ||||| ||||| ||||||||||| || ||||||||||| || ||| | ||||| |||||||| ||||||||||| |||||||| || || || |||||||| |
--gtacatgacttacacttagccttcttttg---ctttactttttgggttgctaaacattttccggaatttgatgat------ccagGAGAGTGAAATCAAATGGGCTTCTCGGTGGGACACGTACCTTCTCATGAACGATGATCAAATCCACTGGTTTTCCATCATAAATTCACTTATGATTGTCC

upper sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 6
gtattgctgatt-aaaatcttggctaccaataaactttcacctcatttgttatgatacgttatggcaagtttgttggtact-ttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC
||| | ||  ||  ||||| | |||          | ||  |||   || || | |   || |      |||     || | ||||||||||||| | ||||||||||| ||||||||||| ||||| ||  | ||||| ||||||||||||||||||||||||||||| ||||||||||||||||| |
gtaattctttttcgaaatccttgct----------tgtcttctcccatgatacggttttttttacttgtttttgccttattattttcagGAAAGTAACATCAAATGGGCTTCACGGTGGGATACATACCTCCTTATGAACGATGATCAGATCCACTGGTTCTCCATCATAAACTCTCTGATGATTGTCC

upper sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
lower sequence: EDP05803 (Chlamydomonas reinhardtii), 3'ss of exon 5
---------------gtattgctgattaaaatcttggctaccaat---aaactttcacctcatttgttatgatacgttatggcaagtttgttggtact--ttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC
                 ||    | |   |    ||| |   |     |  | || ||| |||      ||    ||  | ||   |||| ||||       | ||||  || || |||   ||||| || || |||||||| || ||  | ||||  || || ||||| |||||||||||||||||||||||  |||||||||| |
gcggtgaccggaaacccatgctgggtctgagcactgggtctgagcgcgaggccttgaccgcatcc----tgggctgtccttgc---tttgctggtggcgacgtgcagGCTAGCGAGATCCGCTGGGCCTCGCGCTGGGACACCTACCTGCTGATGATGGACGACCAGATTCACTGGTTCTCCATCATTAACTCGGTGATGATTGTCC

upper sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S24_182V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------gtattgctgattaaaatcttggctaccaataaact--ttcacctcatttgttatgatacgttatggcaa-gtttgttggtactttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC
             ||| || |  || |  |  |   | || || ||    |  | |||| ||| | | |   |  | || || |||      | | | | |||   |||||  | || |||||||| |||||||||||||||||  | | | | ||||| |||||||| ||||| || ||||| || ||  ||||||||||||
tatgcgtaatgtagtagtgatctttgattttatcttttcccatgaagggatcgagctcacttgatgtca---gcgaaggtaatgttcacgttttcatgtgcagCTCAGTGAGGTGAAGTGGGCATCCCGGTGGGACACATATCTACTGACGCAAGATGACCAGATCCATTGGTTTTCAATCATCAATTCCTTGATGATTGTTC

upper sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S140_64V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------gtattgctgattaaaatcttggctaccaataaactttcacctcatttgttatga----tacgttatggcaagtttgttggtactttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC
                      ||  |||| || |   | |  | |   | |||  |||||  || | || | |      ||  || |  |||  || |  || |||   ||| | ||| || |||||||||| || || ||||| ||||||||  | ||||  ||||  ||||| ||||||||||||||||| ||||| || |||||||| |
gtgagaaattcgtctcataaccgttctgctcatcatg-tgtgaggttgaattaatttttcatgtcttgtgctttcgaatctattttctaacaatattttatgtgcttacgcagTACAGTCATGTCAAATGGGCTTCTCGCTGGGATACATATCTACTCATGACAGATGCGCAGATTCACTGGTTCTCCATCATCAACTCCCTCATGATTGTGC

upper sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------------------------------------------gtattgctgattaaaatcttggctaccaataaactttcacctcatttgttatgatacgttatggcaagtttgttggt-acttttt------cagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC
                                                                                                   |||  |  | | ||| |  ||||| | | || | |  |   ||   |   | | |   |   ||||    | | |  |||| |      ||||||||||| ||||| |||||||| || ||||| |||||| | || ||||  |||||||| || || |||||||||||  ||||||| || |||||||| |
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgt-agaatgtcagctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC

upper sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S73_94V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------------------------------------------------gtattgctgattaaaatcttggctaccaataaac-tttcacctcatttg-------ttatgatacgttatggcaa--gtttgttggtactttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC
                                                                                                       | || ||  | |  || |   |        ||   ||||| |||  ||        || |||| | |||||   |  ||| |          | ||| ||||||||||||| |||||||| || ||||| |||||| | || ||||  || || || ||||| ||||||||||||||||| || || |||||||| |
gtgaaatgagttctttaactcgcttttatgttactttacctcttaaaacctttttttttgttaaaaacttctccacttgtgaacagatgagggtatctcgtttggatcgcgaagtgtaaaccatgtattggtcaagtgtttcaactctgttcctcgactttctgat-ctttatgcatatggttcgcctcgtgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACAGACGACCAAATCCATTGGTTCTCCATCATTAATTCCCTCATGATTGTGC

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|308098681|gb|HO760422.1|HO760422
EST:     AAGTTGATACAAGCAAGGATATTGTATTCACATATGATGTTTCCTTCACG                         GAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAAT
genomic: AAGTTGATACAAGCAAGGATATTGTATTCACATATGATGTTTCCTTCACGgtattgctga ... actttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAAT
EST: gi|207840296|gb|GD811343.1|GD811343
EST:     AAGTTGATACAAGCAAGGATATTGTATTCACATATGATGTTTCCTTCACG                         GAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAAT
genomic: AAGTTGATACAAGCAAGGATATTGTATTCACATATGATGTTTCCTTCACGgtattgctga ... actttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAAT
EST: gi|192301746|gb|FG994426.1|FG994426
EST:     CACATATGATGTTTCCTTCACG                         GAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAAT
genomic: CACATATGATGTTTCCTTCACGgtattgctga ... actttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttcacctcatttgttatgatacgttatggcaagtttgttggtactttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC
                                            tactttttc  CT-rich tract
           atttgttat  TA-rich tract