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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcaacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgactcagctatccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG

Basic information

species Arabidopsis thaliana
transcript AT3G08850.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 7
gtattcaacaagaaccat-attcttctgttatgtaaaatgttatgtgtctagattttgactcagctatccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
||| | | | |||||| | || | | | | || | || | | | | ||| | ||| ||||||||||||||||||||||| || ||||| |||||| ||||||| ||| | || || || | ||||||| |||
gtaattgatggcactagccattctttttatagtttagctacctcttctccattttct---ttaatt-tcctaaatttcaattttagGGATGCATGGGACATGGCTGCAGAGATCTGCCTTTCTAAGCTTCCTCAATTAATTGCTGATCCTAATGCAGAGTTTCAG

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 8
gtattcaacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgactcagctatccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
||| | | | || | | | |||| | | ||| ||||| || | ||| | ||| ||||||||||||||||||||||| || ||||| |||||| ||||||| ||| | || || || | ||||||| |||
gtaattgatg-gcactagccattctttttatagtttagctacctcttctgcatttt--ctttaatttcctaaattttaattttagGGATGCATGGGACATGGCTGCAGAGATCTGCCTTTCTAAGCTTCCTCAATTAATTGCTGATCCTAATGCAGAGTTTCAG

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 8
gtattcaacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgactcagctatccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
||| ||| || | | || | || | || | | ||| | || | || |||| | |||||||||||||||||||||||||||| || || ||||| ||||||| || | || || |||| ||||||| |||
gtaactaacctgacttgttctttttt-ttgcattaactaccttttgtgtgatttgtaacat-gctaaa-----------tctcagGGATGCATGGGACATGGCTGCTGAGATTTGCCTTTCCAAGCTTCCTCAGTTAATTGCTGATCCAAATGCAGAGTTTCAG

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 8
gtatt--caacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgact-cagct-at-ccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
||||| | | | | | | || | ||| || ||| | |||||| | ||| | || || ||| | ||||||||||||||||||||||||||| |||| || ||||| ||||| | ||| ||| || | | || || |||
gtattgttggtgattatttttatgatatttttttctaaacgtgttgt---caaattttgtcaacagtttatgtttttatctgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAG

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 8
gtattcaacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgact-cagctatccgttgcat--gcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
||||| || | || | | | | | ||| | | ||||| | ||| | || || || | ||||||||||||||||||||||||||| |||| || ||||| ||||| | ||| ||| || | | || || |||
gtattgttggtgattattgttatgataatttttttctaaacgtgttgccaacttttgtcaacagtttatgtttttatccgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCATCTTTAGTTGAGGATCCTAATTCTGAATTTCAG

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 8
gtattcaacaagaaccatattcttctg-ttatgtaaaatgttatgtgtctagattttgactcagctatccgt-tgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
||| | || || | || ||| || |||| | || | | | || | || | |||||||||||||||||||||||||||||||| |||||||||||| | | ||| || || | ||||||| |||
gtacctactggaaatactagataagtaattttgttaagtgttcaataatccatttgtctcataatgtgccatgcatgtgtgctatagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTAAGTCATTGGTTGATGATCCCAATGCAGAGTTTCAG

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------------------------------------------------gtattcaa--caagaaccatattct--tctgttatgtaaa-------atgttatgtgtctagattttgactca------gctatccgttgcatgctttt-cagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
|| || | | ||| || | || | | | || || | | | | || || || | | || || ||||||| |||| |||||||||| |||||||||||||| |||||||| ||| | || | | || || |||| | ||||| |||
gtacgcttgttctctcatactttcttgcttcctccttttcattcccccttttcttgaaatatattttcctctttacctctctcggtctttttgtgtttaggttatgaagaatttcctaatttataatacgaatgaaattgcttcgtctacccgaatcttctctgatagaacacattctgtgtgttgcttttgcagGCATGCATGGGATATGGCTGCTGAAATTTGTCTTTCACAGTTGCCTGCATTGGTGGATGATCCAAATGCTGAGTTTCAG

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S124_156V6.1 (Physcomitrella patens), 3'ss of exon 8
----------gtattcaacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattt--tgactcagctatccgttgcatgctttt----cagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
| | || | ||| || | || | || | | | ||| ||| | | | ||| ||| |||| |||| | |||||||| |||||||||||||| |||||||| ||||| || | | | ||| |||| | || || ||
ttccttcattgaagcatcttgaaaatgtcatctaatgcaacagaataccttttccaccaaattttcctgatgta-ccacattttgtatgtttttttcgcagGCACGCATGGGATATGGCTGCTGAAATTTGTCTTTCGCAGCTGCCTGCATTGCTAGAGGATCCAACTATTGAATTTCAT

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|116411083|gb|EG453675.1|EG453675
EST:     AATCCAATATCTCACCCTATGCTGCCTCCTACGCATCAACATCATATGTG                         GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACT
genomic: AATCCAATATCTCACCCTATGCTGCCTCCTACGCATCAACATCATATGTGgtattcaaca ... tgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACT
EST: gi|116411080|gb|EG453672.1|EG453672
EST:     AATCCAATATCTCACCCTATGCTGCCTCCTACGCATCAACATCATATGTG                         GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACT
genomic: AATCCAATATCTCACCCTATGCTGCCTCCTACGCATCAACATCATATGTGgtattcaaca ... tgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaaaatgttatgtgtctagattttgactcagctatccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG
                      ttttgac  putative branch site (score: 3)
 tgcttttc  putative PPT
 aatgttat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcaacaagaaccatattcttctgttatgtaaaatgttatgtgtctagattttgactcagctatccgttgcatgcttttcagGGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT