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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGAAATTTCCCCAACCGTATCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAAGGgtgggtgtcttcttctgtcctaagtttctgcacgagacaagttttgagacttgatttgtcaaaatatctttgattttcag

Basic information

species Arabidopsis thaliana
transcript AT1G10290.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 9
AAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGAAATTTCCCCAACCGTATCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAAGGgtgggtgtcttcttctgtcctaagttt----ctgc-acgagacaagttttgagacttgatttgt-caaaata----tctttgattttcag-
   |||||||||||||||||||||||||||||| || |||||  |  | || || ||||| ||| |||| || || |||||||| | |||||||||||||||  |  |    | | ||   | | ||    || | |  || ||  ||   |   || ||     |  || |    ||| |||  |||   
GTCTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGGAAATTCCCAGAGAGAATTAAACAGCTGCCACTGGACAGGCACTTTGACCTCAGCAATGTTAAAAGGgtaag-attggatccagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgacattctag

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA07G40300.1 (Glycine max), 5'ss of exon 9
AAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGAAATTTCCCCAACCGTATCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAAGGgtgggtgtcttcttctgt-cctaagtttctgcacgagacaagttttgagacttgatttgtcaaaatatctttgattttcag-----------------------------
 | |||||||||||||||||| ||||||||||| ||||| || ||| | |||||||| |||||  | || ||||| |||||| | |||||||| || |||||     |  ||   ||    |    |  ||     |   | ||| |    ||   || ||   | |  |  | |  |                                
TAATGGTTGGAAAGTTGTTGCTAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATCGACAGACACTTTGACATAAACAATGTCAAGAGGgtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattttattctcttgacacttgaggtgcttgcttctatattcccattttggcttatttcag

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA17G00480.1 (Glycine max), 5'ss of exon 9
AAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGAAATTTCCCCAACCGTATCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAAGGgtgggtgtcttct------tctgtcctaa-gtttctgcacgagacaagtt-----------ttgagacttga----tttgtcaaaatat-----ctttgattttcag
 | |||||||||||||||||| ||||||||||| ||||| || ||| | |||||||| |||||  | || ||||| |||||| | |||||||| || |||||   | |  ||       | |||| ||  ||||  | |  | | |  |            |||| |||||      |||     ||||      ||||  ||||||
TAATGGTTGGAAAGTTGTTGCCAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATTGACAGACACTTTGACATAAACAATGTCAAGAGGgtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctgttgacacttggggtgcttgcttctatattctcattttggctttcag

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 5'ss of exon 9
AAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGAAATTTCCCCAACCGTATCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAAGGgtg------ggtgtcttcttctgtcctaagtttctgcacga-----gacaagttttgagacttgatttgtcaaaatatctttgatt--ttcag------
   ||||||||| || ||||| |||||||| || ||||| || ||| | ||||||||||| || || || || ||||||||| | |||||||| ||||||||         ||| || ||| |||  || ||| | |   |     ||  | |||||||   | |||  |   | |   |||      ||  |      
TGCTGGTTGGAAGGTCGTTGCCAGTTTTGAGGGGAATTTTCCTAACAGGATCAAGCAGCTCCCTTTAGACAGGCATTTTGACATCAACAATGTCAAAAGGgtatctaccattgtgttgttcggtctcaattttatactatattttggattatttttgaggtctaattactttgagtgattttcccccatttggtcacag

upper sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 9
AAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGAAATTTCCCCAACCGTATCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAAGGgtgggtgtcttcttctgtcctaagtttctgcacgagacaagttttgagacttgatttgtcaaaatatctttgattttcag-----------------------
 || ||||||||||||||||||||||||||||| |||||||||||| | ||||||||||| || || |||| |||||||||  | |||||||| ||||| ||  | ||  |||| | | | |  || |  |    |      ||| | |  || | |   ||    | | |  ||| ||                        
TAGCGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAACAGGATCAAGCAGCTACCTTTAGATAAACATTTTGATATAAACAATGTCAAAAGAgtatg-gttctcttttattc-acattccaacttttgt--gccttttaaatatgttgttgtaaggcctttattgtttgcaatgttccttttcaattgataccag

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|164237558|gb|ES093240.1|ES093240
EST:     ACCTGAACAATGTTAAAAGG                         GTTGTTTTGGAGGCAGATGGTTATCAACCTTACCTTATATCTCCAGAGAAA
genomic: ACCTGAACAATGTTAAAAGGgtgggtgtct ... tgattttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAA
EST: gi|47831974|gb|CK121658.1|CK121658
EST:     TCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAAGG                         GTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAA
genomic: TCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAAGGgtgggtgtct ... tgattttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGAAATTTCCCCAACCGTATCAAGCAGCTTCCATTGGATAGACATTTTGACCTGAACAATGTTAAAAGGgtgggtgtcttcttctgtcctaagtttctgcacgagacaagttttgagacttgatttgtcaaaatatctttgattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT