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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaagatgcttaaaccggatttagtccatttacttttgtttctgcactttgattttggttttaagcttcacctggat...

Basic information

species Arabidopsis thaliana
transcript AT3G51260.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os08g43540.1 (Oryza sativa), 5'ss of exon 1
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaagatgcttaaaccggatttagtccatttacttttgtttctgcactttgattttggttttaagcttcacctggat
| |||||||| ||||| |||||||||||||| ||||||||||| || || |||||||||| |||||| |||||||||||||| ||||||||||| ||||||||   |    | | |  ||  | |      | |   |||||| |   ||    |   | | |    | |    ||   |                    
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACACCGTCGTCCTCGGCGTCGAGAAGAAATCCACCCCCAAGCTCCAGGACTCCAGgtaaatccttcaacccgccccctcc------ccttcgccggatctcacccgcgga---tcgatctcccccccaaatccag--------------------

upper sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os09g36710.1 (Oryza sativa), 5'ss of exon 1
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaagatgcttaaaccggatttagtccatttacttttgtttctgcactttgat-tttggttttaagcttcacctggat
| |||||||| ||||| |||||||||||||| ||||||||| | || || |||||||||| |||||| ||||| |||||||| ||||||||||| ||||||||   |  |     ||  |||         ||    ||  ||  |  ||  |   | |  | ||  |  |  |   || | ||   ||            
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacc-catcacctcctcgcgac--------ctctctccccatacacccccatagatctcatctcgccggtgggggattcgattcgcag------------

upper sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G042604_T01 (Zea mays), 5'ss of exon 1
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaagatgcttaaaccggatttagtc-catttacttttgtttctgcactttgattttggttttaagcttcacctggat
| |||||||| ||||| ||||||||||| || ||||||||||| || || |||||||||| |||||| ||||| ||||| || ||||||||||| ||||||||     ||  ||  | ||        || ||   ||| ||| | |      |  | |     |     || |||     ||||    || |  || |  
AGGCCGTCCGCAAGGGCAACGCCGCCGTGGGCGTCCGCGGCACGGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACACCCAAGCTCCAGGACTCCAGgtagcaaacccctccgtccctcctttctatcctccgaccagatctcgcgatcctcgcctcaaactactatctctgacccgagtttccgtctcc--ctag--

upper sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G138128_T01 (Zea mays), 5'ss of exon 1
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaagatgcttaaaccggatttagtccatttacttttgtttctgca-ctttgattttggttttaagcttcacctggat
| |||||||| ||||| |||||||||||||| ||||||||||| || || ||||||||||  || || ||||| || ||||| ||||||||||| ||||||||     ||   |    |    |   ||| ||   ||| ||| | |    |      |         | || |||    |  || | |  || || |   
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACGGACACCGTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaaccctccgtccctcccatc-gatcctccgaccagatctcgcgattcccgactcaaactaatatctctgaccccgaattcatgtctccccag---

upper sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G050467_T01 (Zea mays), 5'ss of exon 1
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgt-attgctccgatctctaccgatacaagatgcttaaaccggatttagtccatttacttttgtttctgcactttgattttggttttaagcttcacctggat
| |||||||| ||||| |||||||| ||||| ||||||||    || || |||||||||| |||||| ||||| |||||||| ||||||||||| |||||||   | |  || |  || ||  | |         |  || ||| |          |    |   |  |||    ||  |      ||   || ||     
AGGCCGTCCGCAAGGGCAACGCCGCTGTCGGCGTCCGCGGTGTCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtcggtccgtcggtacctccccctccctcccatcca--ccagatct--cttgaccccgggcgccgcctcacccaaatcctcccccaaaaaatctccgcag-

upper sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA02G05190.1 (Glycine max), 5'ss of exon 1
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaaga--tgcttaaaccggatttagtccatttacttttgtttctgcactttgattttggttttaagcttcacctggat-
|||||||||| ||||| |||||||||||||| ||||||||||| || |  |||||||||| |||||| |||||||||||| | |||||||| || ||||||||   ||   |    || | || |      | | |   ||  |||  ||   || |        | |    |||| |    |     |  ||| |       
AAGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACAACGTCGTCCTCGGCGTCGAGAAGAAATCCACCGCCAAGCTCCAAGACTCCAGgtaccact---actcttatcaattcccccctttcctttcccttattaggttttttaatcggcaaatgttagttttgttagcagagaggattttccctcttccc

upper sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA16G23580.1 (Glycine max), 5'ss of exon 1
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaagatgcttaaaccggatttagtccatttactttt--gtttctgcactttgattttggtt-ttaagcttcacctggat----
|||||||||| ||||| |||||||||||||| ||||||||||| || | ||| ||||||| |||||| |||||||||||| | || ||||| || |||||||| | ||   |    |  | || |||    ||    |||  |    ||| ||| |  ||   || ||     || |    |     || |  | |   |||     
AAGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACAATGTTGTCCTCGGCGTCGAGAAGAAATCCACCGCCAAACTCCAAGACTCCAGgtactact---actcttttcaattcaattccct----ccgtttcagatccctttccccttcgattactagggattaaccaagaaaactacgtgttataaggagaagg

upper sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv03s0038g02300.t01 (Vitis vinifera), 5'ss of exon 1
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccga-tctctaccgatacaagatgct--taaaccggatttagtccatttacttttgtttctgcactttgattttggttttaagcttcacctggat
|||||||||| ||||| |||||||||||||| ||||||||||| || ||  ||||||||| |||||||||||| |||||| ||||||||||||| ||  ||||   |||    |||||||   |||    |     | |    | ||||      | | || ||  || ||  ||  |  |   | | | | ||    |||  
AAGCCGTCCGTAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACACCATCGTCCTCGGCGTCGAAAAGAAGTCCACCGCTAAGCTCCAGGACTCTCGgtacctctcttcctctctacgattacgcattttcagtgattgtggtttaagatcgtgaattctgagtcagcttttgaacct--atctgatggtttctgtggc-

upper sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv04s0023g03690.t01 (Vitis vinifera), 5'ss of exon 1
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaagatgcttaaaccggatttagtccatttacttttgtttctgcactttgattttggt--tttaagcttcacctggat
|||||||||| || || |||||||||||||| ||||||||||| || ||  |||| |||| |||||| || || |||||| | || ||||| |||||||||| |   |      | |  |  |   |  | |||        ||  ||  ||       ||    |    || |  |||| |  |||  |   || |    |
AAGCCGTCCGTAAAGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACACCATCGTTCTCGGCGTCGAGAAAAAGTCCACCGCCAAACTCCAAGATTCCAGgtctccttttttcatttttcatttttattttcttt--ttttcttgtgtaaataccaaaatgaaggtagggttagggtttgatggttttggagacatccatgt

upper sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ31080 (Selaginella moellendorffii), 5'ss of exon 1
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaagatgcttaaaccggatttagtccatttacttttgtttctgcactttgattttggttttaagcttcacctggat
| ||||| || ||||| |||||||||||||| ||||||||||| || ||  |||| |||| ||| || |||||||||||| | |||||||||||  | |||| | | | |  |||            |||   || |||   | |||     |  ||  || ||| | | | |   |   |                   
AGGCCGTGCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACAATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgt-tcgtttccctct------------gatctctagacc---tctagatttctagctcctgattccgaaatctctgtccag-------------------

upper sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaagatgcttaaaccggatttagtccatttacttttgtttctgcactttgattttggttttaagcttcacctggat
| ||||| |||||||| |||||||||||||| ||||||||||| || ||  |||| |||| ||| || |||||||||||| | |||||||||||  | |||| | | | |  |||            |||   || |||   | |||     |  ||  || ||| | | | |   |   |                   
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgt-tcgtttccctct------------gatctctagacc---tctagatttctagctcctgattccgaaatctctgtccag-------------------

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|152033955|gb|BP821148.2|BP821148
EST:     GTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAG                         ATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGC
genomic: GTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctcc ... tgcttctcagATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGC
EST: gi|124720591|gb|EH811993.1|EH811993
EST:     CCCTAAGCTCCAGGATTCCAG                         ATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGC
genomic: CCCTAAGCTCCAGGATTCCAGgtattgctcc ... tgcttctcagATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGC
EST: gi|125018080|gb|EL090349.1|EL090349
EST:     CCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAG                         ATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGC
genomic: CCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctcc ... tgcttctcagATCAGCAAGGAAGATAGTGAGCCTTGATAATCACATTGCATTGGCCTGTGC
EST: gi|164131609|gb|ES149385.1|ES149385
EST:     GTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAG                         ATCAGCAAGGAAGATAGTGAGCCTTGATAATCA
genomic: GTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctcc ... tgcttctcagATCAGCAAGGAAGATAGTGAGCCTTGATAATCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaagatgcttaaaccggatttagtccatttacttttgtttctgcactttgattttggttttaagcttcacctggat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgatctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcacct