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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgttaacgtttgcttcttcattttcagGTCAATACAGGTGCTAAAGACAACAAGATGCAAAGCTTCTTCTTAGCTGAGACTCTTAAGTATCTATATCTTCTCTTTTCGCCTTCATCTGTTATTTCAT

Basic information

species Arabidopsis thaliana
transcript AT1G51590.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 13
gtaag---tttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgttaacgtttgcttcttcattttcagGTCAATACAGGTGCTAAAGACAACAAGATGCAAAGCTTCTTCTTAGCTGAGACTCTTAAGTATCTATATCTTCTCTTTTCGCCTTCATCTGTTATTTCAT
|||||   |||  |   |   | |   || | |  || |         | | || ||  |    |    |  | |||  || ||  |   |  ||  |  | | ||||| ||||| || |  || || |||| |||||||||||||||| |||| |||||||| ||||| ||||| || || || || ||| |||| || || || |
gtaagctttttttaattgtttttatgatagc-atccatacttaaattcccactgagcgctagtgtaagacttacacaaattcttgtcaaatattt--tggtctccagGTGAATACTGGCGAGAAGGATAACATGATGCAAAGCTTCTTCCTAGCAGAGACTCTCAAGTACCTATACCTCCTGTTCTCTCCTCCATCAGTCATATCCT

upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 12
gtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaa-acacgt-tgttaacgtttgcttcttcattttcagGTCAATACAGGTGCTAAAGACAACAAGATGCAAAGCTTCTTCTTAGCTGAGACTCTTAAGTATCTATATCTTCTCTTTTCGCCTTCATCTGTTATTTCAT
     | | |   |         ||| | |||     ||   | |  |||    |   | |   ||| |   || | | | |||    ||| |||    || |||||| ||||  || |  |||||||||| |||||||||||||||  | || ||||| || |||||| | ||||||||||| || ||||| ||||| ||  |||
-----tcttgcttcttttgatatttatctaatgctggacaaccatttagtatctcaagctactattctgcctactcatgtattataacttg-ttcacatttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAGACCCTGAAGTATTTTTATCTTCTCTTCTCACCTTCTTCTGTCATCCCAT

upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 13
gtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaa-acacgt-tgttaacgtttgcttcttcattttcagGTCAATACAGGTGCTAAAGACAACAAGATGCAAAGCTTCTTCTTAGCTGAGACTCTTAAGTATCTATATCTTCTCTTTTCGCCTTCATCTGTTATTTCAT
     | | |   |         ||| | |||     ||   | |  |||   ||   | |   ||| |   || | | | ||| |  ||| |||    || |||||| ||||  || |  |||||||||| |||||||||||||||  | || ||||| || |||||| | ||||||||||| || ||||| || || || ||||
-----tcttgcttcctttgatatttatctaatgctggacaaccatttagtatcccaagcaactattctgcctactcatgtattatcacttg-ttcacatttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAGACCCTGAAGTATTTTTATCTTCTCTTCTCACCTTCTTCAGTCATCTCAT

upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 13
gtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgttaacgtt--tgcttctt--cattttcagGTCAATACAGGTGCTAAAGACAACAAGATGCAAAGCTTCTTCTTAGCTGAGACTCTTAAGTATCTATATCTTCTCTTTTCGCCTTCATCTGTTATTTCAT
 |  | |  |   |||| |  | ||  |        |  | | ||   ||   |   | ||||| |      | | ||| | ||  |  || ||||    |||  ||||| ||||  ||||  |||||||| | |||||||||||||||| | |||||||| || || ||||| |||||||| || || |||||  | || |||||||
cttggctgtg---cgggttatcattttctttcattgttactttcttttgtttactgctacatctgt-----gctctttgcttactctgctggttctgggtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAGACACTCAAATATCTCTATCTTCTTTTCTCACCTTCGACGGTCATTTCAT

upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgttaacgtt--tgcttctt--cattttcagGTCAATACAGGTGCTAAAGACAACAAGATGCAAAGCTTCTTCTTAGCTGAGACTCTTAAGTATCTATATCTTCTCTTTTCGCCTTCATCTGTTATTTCAT
 |  | |  |   | || |  | ||  |        |  | | ||   ||   |   | ||||| |      | | ||| | ||  |  || ||||    |||  ||||| |||| ||  |  |||||||| | |||||||||||||||| | |||||||| || || ||||| |||||||| || || ||||| || || |||||||
cttggctgtg---ctggttatcattttctttcattgttactttcttttgtttactgctacatctgt-----gctctttgcttactctgctggttctgggtattcacagGTAAATAGAGACGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAGACACTCAAATATCTCTATCTTCTTTTCTCACCTTCGTCAGTCATTTCAT

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|116428419|gb|EG471011.1|EG471011
EST:     CATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGAT                         GTCAATACAGGTGCTAAAGACAACAAGATGCAAAGCTTCTTCTTAGCTGAG
genomic: CATTTGAGAAGAACTCTCGCGTAGAATCTGGATATGTAGGCTTGAAGGATgtaagtttcg ... tcattttcagGTCAATACAGGTGCTAAAGACAACAAGATGCAAAGCTTCTTCTTAGCTGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggcctttccatctttcggaaacacgttgttaacgtttgcttcttcattttcagGTCAATACAGGTGCTAAAGACAACAAGATGCAAAGCTTCTTCTTAGCTGAGACTCTTAAGTATCTATATCTTCTCTTTTCGCCTTCATCTGTTATTTCAT
                            tgttaac  putative branch site (score: 2)
                                    tttgcttcttcatttt  CT-rich tract
                                            ttcatttt  TA-rich tract