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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacttgaaccgtttcctcagctgcacatttatttgtgtcttaaatatcaagtcaacaagcttgtttagcagtcttgcggataacaattcttcttttcagGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATGATGAGGATACCGGTACAGTTGGTGTGGTTGACCCTTCTGAAGCTGTACCTGTTATGGATG

Basic information

species Arabidopsis thaliana
transcript AT1G06130.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g34100.1 (Oryza sativa), 3'ss of exon 2
ttacttgaaccgtttcctcagctgcacatttatttgt-gtcttaaatatcaagtcaacaagcttgtttagcagtc-ttgcggataacaattcttcttttc----agGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATGATGAGGATACCGGTACAGTTGGTGTGGTTGACCCTTCTGAAGCTGTACCTGTTATGGATG
   |||     | || |   ||| | |||  |   ||  |     ||| | |      ||   | | ||| | |  ||||  | ||   || | ||| |     |||| || || |||   || ||||||||||| ||| |||||||||  ||||| || |||||||| || || ||||||||||||||    ||  | ||  |||
---ctta---tgctttccttgcttcgcataaaagggttattggggatagctacattggaattatctatagtatttgttgccaacaatgtttatgcttcttgtgtagGTACCCTGCCTTCAAGATAACTATGCTTACATCCTACATGATGTTGATACTGGAACAGTTGGAGTTGTGGACCCTTCTGAAGCAACGCCAATCATAAATG

upper sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 2
------------------------------------------ttacttga--accgtttcctcagctgcacatttatttgtgtcttaaatatcaagtcaacaagcttg---tttagcagtcttgcggataacaattcttcttttcagGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATGATGAGGATACCGGTACAGTTGGTGTGGTTGACCCTTCTGAAGCTGTACCTGTTATGGATG
                                           || | ||  ||  ||   ||| | |  |   ||  | | ||| ||  |  | |   | ||||||    | |  |  | ||| |  | | |||| || || | |||| || || || | |||||| ||||||||| | |||||||||| ||| || |||||||||||||| ||||| |||||||||||||| ||| | || ||||
gtgagagcaggtctcttatcagtcttttctgttttcatagtgctattggattacaattaggtcacccgtgctgataagttt-tctgaagaaatatgatga-aagcttaagttctgacgttattgtgtttta-aattttttttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTATCATAGATG

upper sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G03320.1 (Glycine max), 3'ss of exon 2
---------------------------------------ttacttgaaccgt---ttcctcagctgcacatttatttgtgtcttaaatatcaagtcaacaagcttgtttagcagtc-ttgcggataacaattcttcttttcagGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATGATGAGGATACCGGTACAGTTGGTGTGGTTGACCCTTCTGAAGCTGTACCTGTTATGGATG
                                           ||| |   |   |   ||| | |  |   ||  | | ||| ||  |  | |   | |  ||   ||   | |  |||    ||| ||    | || | |||| || || || | |||||| ||||| ||| | ||||||||||  ||||| |||||||||||||| ||||| |||||||||||||| ||||| || ||||
gtgagagcgggtctcttattagttttcagttgctgtggtcctgttggattataaataggtcacccgtgctgataagttt-tctgaagaaatatgctgaaagcctaaattgtgacttattgtctttaaaaaaaaatattgttagGTACCTTGCCTGAAGGACAATTATGCATATCTGTTACATGATGTAGATACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTGTCATAGATG

upper sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G13470.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------ttacttgaacc--gtttcctcagctgcacat-ttatttgtgtcttaaatatcaagtcaacaagcttgttta-gcagtcttgcggataacaattcttctttt-------cagGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATGATGAGGATACCGGTACAGTTGGTGTGGTTGACCCTTCTGAAGCTGTACCTGTTATGGATG
                                                   | | | |    ||  |   || ||| ||   || |    |||  |  |  | |   | |  || || |  || || || |  ||  || || |  ||||        |||| ||||| |||| |||||| ||||| ||| | ||||| |||| |||||| || ||||||||||| ||||| ||||||||||||| |||| | || ||||
gtgagcagatctcttcttccttttttaaaggtttttttgtgatgcaattagattagtatttagtcactcaagttgctcaagctaataagctctggagcaatatgctgaaattctagtgtgtgctgtgttacttatctcatttttctttttgaattgttagGTTCCATGCCTTAGGGACAATTATGCATATCTTTTACACGATGTGGATACGGGGACAGTTGGTGTTGTTGATCCTTCTGAAGCTGCACCTATCATAGATG

upper sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G05470.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------ttacttgaacc--gtttcctcagctgcacat-ttatttgtgtcttaaatatcaagtcaacaagcttgttta-gcagtcttgcggataacaattcttcttt----tcagGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATGATGAGGATACCGGTACAGTTGGTGTGGTTGACCCTTCTGAAGCTGTACCTGTTATGGATG
                                                 | | | |    ||  |   || ||| ||   || |    |||  |     | |   | |  || |  |  || || || |  ||  || || |  ||     | |||| |||||||||| |||||| ||||| ||| | ||||| |||| |||||| || ||||||||||| ||||| ||||| |||||||  ||| | || ||||
gtgagcagatctcttcttcctttttataaggcttttgtgatgcaattagattagtatttagtcactcaagttgctcaagctaataagctctggagccatatgctgaaatcctagcatgtgctgtgtttcttatctcatttttctttaattgttagGTTCCATGTCTTAGGGACAATTATGCATATCTTTTACACGATGTGGATACGGGGACAGTTGGTGTTGTTGATCCTTCCGAAGCTGCGCCTATCATAGATG

upper sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 4
-ttacttgaaccgtttcctcagctgcacatttatttgtgtcttaaatatcaagtcaacaagcttgtttagcagtc--ttgcggataacaattcttcttttcagGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATGATGAGGATACCGGTACAGTTGGTGTGGTTGACCCTTCTGAAGCTGTACCTGTTATGGATG
 ||| ||||  |  ||  | |  |    ||| | | |  |  |||   |    |           || |    |   |    |  |||  ||    | ||||||| |||||||| | |||||||||||| ||| | |||||||| |  ||||| || |||||||| || ||||| ||||||||||| ||||||||||| ||||
cttaattgactcacttggtaactta---attgactcgcttggtaacagttctttttgtgcttcctttcacacataaatctttgtcaactttttccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATG

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|125269785|gb|EL283870.1|EL283870
EST:     TGTCTCTTCCTCATTGCAAATTGAACTG                         GTGCCATGTCTTACGGACAACCATGCTTATATCTTACATGATGAGGATACC
genomic: TGTCTCTTCCTCATTGCAAATTGAACTGgtttgtgtgt ... ttcttttcagGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATGATGAGGATACC
EST: gi|125207425|gb|EL222379.1|EL222379
EST:     ATTCTGCAGTGTCTCCAATGTCTCTTCCTCATTGCAAATTGAACTG                         GTGCCATGTCTTACGGACAACTATGCTTATATCTTACATG
genomic: ATTCTGCAGTGTCTCCAATGTCTCTTCCTCATTGCAAATTGAACTGgtttgtgtgt ... ttcttttcagGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcaagtcaacaagcttgtttagcagtcttgcggataacaattcttcttttcagGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATGATGAGGATACCGGTACAGTTGGTGTGGTTGACCCTTCTGAAGCTGTACCTGTTATGGATG
                                 ggataac  putative branch site (score: 3)
                                       caattcttcttttc  CT-rich tract
                                   ataacaatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacttgaaccgtttcctcagctgcacatttatttgtgtcttaaatatcaagtcaacaagcttgtttagcagtcttgcggataacaattcttcttttcagGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATGATGAGGATACCGGTACAGTTGGTGTGGTTGACCCTTCTGAAGCTGTACCTGTTATGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG