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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctaaatctttttctctctgatctaagccgttctgttcaaccctgtatctatggttgttggaagtattattgatactggtcatggagatagctatattcggatctggctcattcagaaaatacattttcagGAAAAGAGGAGTATCCGCCCTACTTTTTCAGCTGAGAAGATCTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGG

Basic information

species Arabidopsis thaliana
transcript AT1G52360.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 12
gtttctaaatctttttctctctgatctaagccgttctgttcaaccctgtatctatgg-ttgttggaagtattattgatactggtcatggagatagctatattcggatctggctcattcagaaaatacattttcagGAAAAGAGGAGTATCCGCCCTACTTTTTCAGCTGAGAAGATCTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGG
                           | | | || | || |    | |  | | |  |||       ||||  || |     | ||  | || | ||| ||| | | ||  | || ||        || | ||||| ||||  | ||| |||||||| |||||||||||    || ||||| ||||  || || || |||||||| ||||||||||| ||||||||||| ||||
-------------------------taaggaccttttattaatgaatttggcaaagaattgcacatcatatt-ctgttggcatttatcaatattg-tatcttctggtttgaatgatcca--------atatgcagGAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGG

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G095348_T03 (Zea mays), 3'ss of exon 12
gtttctaaatctttttctctctgatctaagccgttctgttcaaccctgtatctatggttgttggaagtattattgatactggtcatggagatagctatattcggatctggctcattcagaaaatacattttcagGAAAAGAGGAGTATCCGCCCTACTTTTTCAGCTGAGAAGATCTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGG
                    |  || | |    |    |  | || | | ||            ||| |      || ||  || |   | ||     |||    | || || |   |  |  |   ||||||||| ||||  | |||||||||| | |||||||| |||   || ||||| ||    ||||| || |||||||| ||||||||||||||||||||||| ||||
-------------------gcaaatgtgaagtttctgatctagccatatttc-------acaaaaagcac-----attctaatcttttgg-tattctcattgtcctgtgacttaa--attatctgatttttcagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGG

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 12
gtttctaaatctttttctctctgatctaagccgttctgttcaaccctgtatctatggttgttggaagtattattgatactggtcatggagatagctatattcggatctggctcattcagaaaatacattttcagGAAAAGAGGAGTATCCGCCCTACTTTTTCAGCTGAGAAGATCTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGG
                                 || ||    | ||| | | |    |  ||   |         ||     || |   |  |  |  |||    ||||   | |  |  |  |   |||| |||| ||||  | |||||||||| | |||||||| |||   || | ||| ||    ||||| || |||||||| ||||| ||||||||||||||||| ||||
---------------------------------ttgtgacatagcctttttttgaattgtttcacaaagaagcacattgcaatcttttgg-cattttcattgtattctgtgacttaaattatctgattttttagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTATGGTGGGGTATTGTTGGCAATGTGTTCTAGTGACTTCATCTGCTTTTATGACTGGG

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 12
gtttctaaatctttttctctctgatctaagccgttctgttcaaccctgtatctatggttgttggaagtattattgatactggtcatggagatagctatattcggatctggctcattcagaaaatacattttcagGAAAAGAGGAGTATCCGCCCTACTTTTTCAGCTGAGAAGATCTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGG
                        ||| |    |    |||   | | |   | | | |||  |    || |   |   ||    | | || || | ||   |||  |||    ||       || |||| |||||||||| ||||||||| || |||||||||||||||   || ||||| || ||  | || || ||||| |||| |||||||||||||||||| |||||||
------------------------tctcaaaaataacattc--tcttattgttttagatgtctgccaaatgaaataagttgtctctaggga-agttttaaatggaaatggaatttt------gtatattt-cagGAAAAGAAGAGTATCCGACCAACTTTTTCAGCTGAGCGAATATTTGGCGGCACTGTATTGGCAATGTGCTCAAATGATTTCATCTGCTTTTACGATTGGG

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 1
gtttctaaatctttttctctctgatctaagccgttctgttcaaccctgtatctatggttgttggaagtattattgatactggtcatggagatagctatattcggatctggctcattcagaaaatacattttcagGAAAAGAGGAGTATCCGCCCTACTTTTTCAGCTGAGAAGATCTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGG
                       |   |   | |||| || |    | ||   |||  |     | | | |||   |  ||    | | || || | || | |||  ||     ||       || |||| |||||||||| ||||||||| || ||||||||||||||    || ||||| || ||  | || || ||||| |||| ||||||||||||||||||||||||||
---------------------caaaaaataacattctctt-attgttttag--atgtcttccaaatgaactataagt--tgtctctaggga-agttttaattggaaatgaaatttt------gtatattt-cagGAAAAGAAGAGTATCCGACCAACTTTTTCAGCTGAACGAATATTTGGTGGCACTGTATTGGCAATGTGCTCAAATGATTTCATCTGCTTTTATGATTGGG

upper sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 12
gtttctaaatctttttctctctgatctaagccgtt-ctgttcaaccctgtatctatggttgttggaagtattattgatactggtcatggagatagctatattcggatctggctcattcagaaaatacattttcagGAAAAGAGGAGTATCCGCCCTACTTTTTCAGCTGAGAAGATCTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGG
                     |  |    |||  |  |||           | |  |||   || || |||  |     ||| ||   || ||            |    | | | | |      |   |||||||||||||||||| |||| || || |||||||||||| | || ||||||||||| || || || ||||| |||| |||||| || || || ||||| ||||
---------------------tattgcctgccactgttgtctggttacaagtgttaggtaaatgcaaatatattc----ctgttcggagaaat---------tcaacagagtttaatgaagtggcat-ctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG

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|19878420|gb|AU239251.1|AU239251
EST:     CGGTTAGAGAAAGCTCATCAAAGATTAAAATATTTAGCAAAAATTTCCAG                         GAAAAGAGGAGTATCCGCCCTACTTTTTCAGCTGAGAAGATCTTTGGAGGA
genomic: CGGTTAGAGAAAGCTCATCAAAGATTAAAATATTTAGCAAAAATTTCCAGgtttctaaat ... acattttcagGAAAAGAGGAGTATCCGCCCTACTTTTTCAGCTGAGAAGATCTTTGGAGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtcatggagatagctatattcggatctggctcattcagaaaatacattttcagGAAAAGAGGAGTATCCGCCCTACTTTTTCAGCTGAGAAGATCTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGG
                                              cattttc  CT-rich tract
                                      agaaaatacatttt  TA-rich tract