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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgccattgtgccttttattactgtctcaataagcaatgtatatgcggctgttgtgttccctggtagctaatcatggtttctgttgttttcttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTGGCAATAGCACAAAACGTTGATACGGGAGCAGTATTGATGCAAGGCTTTG

Basic information

species Arabidopsis thaliana
transcript AT1G31860.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G31860.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0068g00910.t01 (Vitis vinifera), 3'ss of exon 1
--ttgccattgtgccttttattactgtctcaataagcaatgtatatgcggctgttgtgttccctggtagctaatcatggtttctgttgttttcttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTGGCAATAGCACAAAACGTTGATACGGGAGCAGTATTGATGCAAGGCTTTG
        |  |   ||| || ||  | |   |   |    | | | |   | | || | |           |  | ||| ||||      | |  | |||||| || |  ||||| ||| |  | || |||||||||||||| || || ||||||||||| ||||| || || || |||||||| || |||||||||||||
ataatttgtcctctgtttcatcaccattttccttcccttcttttgttccttt-tggtatacaaacaagatggagtaaggtatctgacaggatat-attttagGTTGAAACATTGTTAGACAGTGTGAAGTGGGATGACAAAGGTTTGGCAGTGGCAATAGCCCAAAATGTCGACACAGGAGCAGTTTTAATGCAAGGCTTTG
















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|86029614|gb|DR325367.1|DR325367
EST:     ATGTCGTATTCGSGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
EST: gi|86029609|gb|DR325362.1|DR325362
EST:     ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
EST: gi|86029621|gb|DR325374.1|DR325374
EST:     ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
EST: gi|86029617|gb|DR325370.1|DR325370
EST:     ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
EST: gi|86029619|gb|DR325372.1|DR325372
EST:     ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
EST: gi|86029605|gb|DR325358.1|DR325358
EST:     ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
EST: gi|86029612|gb|DR325365.1|DR325365
EST:     ATGTSGTATTCGSGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATRACAAAGGATTAGCTGTG
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
EST: gi|86029620|gb|DR325373.1|DR325373
EST:     ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
EST: gi|86029611|gb|DR325364.1|DR325364
EST:     ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
EST: gi|86029615|gb|DR325368.1|DR325368
EST:     ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
EST: gi|125099039|gb|EL154989.1|EL154989
EST:     ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATGA
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGA
EST: gi|86029606|gb|DR325359.1|DR325359
EST:     ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
EST: gi|86029616|gb|DR325369.1|DR325369
EST:     ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGSATTAAATGGGATGACAAAGGATTAGCTGTG
genomic: ATGTCGTATTCGCGTGCAATGATAATAAGAACATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
EST: gi|124920736|gb|EH994422.1|EH994422
EST:     CATTGCTCTTCAAGCTAAG                         GTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG
genomic: CATTGCTCTTCAAGCTAAGgtaaacatct ... cttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggctgttgtgttccctggtagctaatcatggtttctgttgttttcttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTGGCAATAGCACAAAACGTTGATACGGGAGCAGTATTGATGCAAGGCTTTG
                    agctaat  putative branch site (score: 3)
                                tttctgttgttttctt  putative PPT
                       taatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgccattgtgccttttattactgtctcaataagcaatgtatatgcggctgttgtgttccctggtagctaatcatggtttctgttgttttcttgtgttagGTAGATAACTTGTTGGACCGCATTAAATGGGATGACAAAGGATTAGCTGTGGCAATAGCACAAAACGTTGATACGGGAGCAGTATTGATGCAAGGCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - -caataag