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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttctattgtcagtttgcttcgttttagttcattatgtcgaatcgagttctaattcgggttttgtctttctccttcagGATTTCCAGCTCGGTGAAACAGTTAGAAGCTTGCCTCATTGTCATCACATGTTTCACTTACCTTGCATAGACAATTGGCTCCTTAGACACGGTTCTTGCC

Basic information

species Arabidopsis thaliana
transcript AT2G17730.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G36760.1 (Glycine max), 3'ss of exon 5
----------------------gttagttctattgtcagttt--gcttcgttttagttcattatgtcgaatcgag--ttctaattcggg-----ttttgtctttctcc----ttcagGATTTCCAGCTCGGTGAAACAGTTAGAAGCTTGCCTCATTGTCATCACATGTTTCACTTACCTTGCATAGACAATTGGCTCCTTAGACACGGTTCTTGCC
                      || | | | | |    || |   | | |   ||  |  || | |   || | |  || | ||    |     || ||  ||| | |    |  |||| ||   ||| || || ||||| ||||||||||||||||| ||||||||||||||| ||||||||||||| || |||||| | ||||| ||||||||||
gttagtttttacactttacatcgtcaataccactagatgtctataccttgaactaaat-gttttctaagattgtgtattgtgatatatgaacatttctgcatttgtgcaatatatagGACTTTATGCTTGGAGAGACAGTAAGAAGCTTGCCTCATTGCCATCACATGTTTCACCTACCTTGCATAGATAAGTGGCTCTTCAGACATGGTTCTTGCC

upper sequence: AT2G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G08540.1 (Glycine max), 3'ss of exon 4
----------------------gttagttctattgtcagtttgcttcgttttagttcattatgtcgaat----cgagttctaattcggg---ttttgtctttctcc----ttcagGATTTCCAGCTCGGTGAAACAGTTAGAAGCTTGCCTCATTGTCATCACATGTTTCACTTACCTTGCATAGACAATTGGCTCCTTAGACACGGTTCTTGCC
                      || | | | | |    || |    |  || |  | | ||| || ||      |  || | ||  |     || ||  ||| | |    |  |||| ||   ||| || || ||||| |||||||| |||||||| ||||||||||||||| ||||||||||||| || |||||| | ||||| ||||||||||
gttagttcttacacttttctttgtcaataccactagatgtctatacc--ttgaactaaatatttctaagattgtgtattgtgatatgaacatttctgcatttgtgcaatatatagGACTTTATGCTTGGAGAGACAGTAAGAAGCTTACCTCATTGCCATCACATGTTTCACCTACCTTGCATAGATAAGTGGCTCTTCAGACATGGTTCTTGCC

upper sequence: AT2G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G05000.1 (Glycine max), 3'ss of exon 4
-------------------gttagttctattgtcagtttgcttcgttttagttcattatgtcgaatcgagttctaattcgggttttgtctttctccttcagGATTTCCAGCTCGGTGAAACAGTTAGAAGCTTGCCTCATTGTCATCACATGTTTCACTTACCTTGCATAGACAATTGGCTCCTTAGACACGGTTCTTGCC
                    ||  || |||| | | ||    | ||  ||    |   |  | || |  |||    ||   ||    | || |   | ||||| || ||||| || || || | |||||| |||||||||||||||||||| |||||| |||||||||| || || |||||  | |  || ||||||||||
agaaaaaaaaacttaggtatttgattttatt-ttatttctggtggtgataaagaaaagttgctaagcttgtttattttattgtgaatttttgcatttgcagGACTTTCAGCTTGGGGAGACTGGTAGAAGTTTGCCTCATTGTCATCACATTTTTCACCTACCTTGCATTGATAAGTGGCTGATCAAGCATGGTTCTTGCC

upper sequence: AT2G17730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0264g00020.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------gttagttctattgtcagtttgcttcgttttagttcattatgtcgaatcgagttctaattcgggttttgtctttctc--cttcagGATTTCCAGCTCGGTGAAACAGTTAGAAGCTTGCCTCATTGTCATCACATGTTTCACTTACCTTGCATAGACAATTGGCTCCTTAGACACGGTTCTTGCC
                             ||     | || | | |        ||| |||   || | | ||| |   || |||||    ||    |||   |   ||||||| || ||||| || || |||||  |||| ||||| |||||||| || ||||||||| | || ||||| || || ||||||||| |||||||||||||||
gtatagccataagttttcctctacataatttctccttcttataaataaataggctttcagtgatttgtatagaagcttatt-taattgaaattggaacttctgcattttcagGACTTTCAGCTTGGAGAGACAGTCCGAAGTTTGCCCCATTGTCACCATATGTTTCACCTGCCATGCATTGATAAGTGGCTCCTTGGACACGGTTCTTGCC

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|86079260|gb|DR375017.1|DR375017
EST:     ATAACACTGATGCTTCTGAGAACACAGACTCATGTTCTGTTTGTCTTCAG                         GATTTCCAGCTCGGTGAAACAGTTAGAAGCTTGCCTCATTGTCATCACATG
genomic: ATAACACTGATGCTTCTGAGAACACAGACTCATGTTCTGTTTGTCTTCAGgttagttcta ... tctccttcagGATTTCCAGCTCGGTGAAACAGTTAGAAGCTTGCCTCATTGTCATCACATG
EST: gi|86081521|gb|DR377278.1|DR377278
EST:     ATAACACTGATGCTTCTGAGAACACAGACTCATGTTCTGTTTGTCTTCAG                         GATTTCCAGCTCGGTGAAACAGTTAGAAGCTTGCCTCATTGTCATCACATG
genomic: ATAACACTGATGCTTCTGAGAACACAGACTCATGTTCTGTTTGTCTTCAGgttagttcta ... tctccttcagGATTTCCAGCTCGGTGAAACAGTTAGAAGCTTGCCTCATTGTCATCACATG
EST: gi|86056622|gb|DR352379.1|DR352379
EST:     ATAACACTGATGCTTCTGAGAACACAGACTCATGTTCTGTTTGTCTTCAG                         GATTTCCAGCTCGGTGAAACAGTTAGAAGCTTGCCTCATTGTCATCACATG
genomic: ATAACACTGATGCTTCTGAGAACACAGACTCATGTTCTGTTTGTCTTCAGgttagttcta ... tctccttcagGATTTCCAGCTCGGTGAAACAGTTAGAAGCTTGCCTCATTGTCATCACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagttcattatgtcgaatcgagttctaattcgggttttgtctttctccttcagGATTTCCAGCTCGGTGAAACAGTTAGAAGCTTGCCTCATTGTCATCACATGTTTCACTTACCTTGCATAGACAATTGGCTCCTTAGACACGGTTCTTGCC
                        ttctaat  putative branch site (score: 2)
                                    ttttgtctttctcctt  putative PPT
     ttcattat  TA-rich tract