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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACTgtaagtatttctcagcttctttggcattgtgttatgatgtgttcttgtataattttatgaatgcataagttagctgtataccatattaaaacgtattgcatcctcaatgtag

Basic information

species Arabidopsis thaliana
transcript AT1G50370.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 5
CTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACTgtaagtatttctcagcttctttggcattgt-gttatgatgtgttcttgtataatt-ttatgaatgcataagttagctgtataccatattaaaacgtattgcatcctcaatgtag
||| || || ||||||||||||||||| ||||| ||||| ||| | |||||||| |||||||||||||| ||||| |||||||| || ||  ||||||| |||||| | | |   | | ||     |||| | | |    | ||  ||   |||  | || ||  |||| | ||    |  |                                
CTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCATTAATGGCACGgtaagtttgtttggacattttgtaagttgtcggtttataatttttgtgccaaataatcatcaaaccatatgctaaaaatccag-------------------------------

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 5
CTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACTgtaagtat-ttctcagcttctttggcattgtgttatgatgtgttcttgtataattttatg-aatgcataagttagctgtataccatattaaaacgtattgcatcctcaatgtag-------------------------
 ||||| |||||||| ||||||||||| ||||||||||||||| ||||||| || |||||||||||||||||||| ||||| || ||||||||||| ||||||| | | || | |   |||    || |           | ||||| | |   | || | | ||   ||| |   | |||   || || ||   | ||  |   | | |                             
TTATGATGAATGCCAGAGGAAGTATGGGAATGCTAATGCTTGGCGATATTGTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTATAGATGGAACTgtaaatctctttttactctctccatcagtcctcctcctatttttcttatgtgcatgtaggcagtggtcaaggtttttttattttattttgaattctgtttgaaaataactaagtcttttatttgctctggttcacttag

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA20G23310.2 (Glycine max), 5'ss of exon 5
CTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACTgtaagtatttctcagcttctttggcattgtgttatgatgtgttcttgtataattttatgaatgcataagttagctgtataccatattaaaacgtattgcatcctcaatgtag
 ||||| |||||||| ||||||||||| ||||| ||||||||| | ||||| || ||||| ||||||||| | |||||||| || ||||| ||||| ||||||| ||| | | | || | |   | |   ||    |      |   | |   | | || ||   |  ||  |  |  |||   ||| |    | |||  |  |   |||  
TTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTATTGATGGAACTgtaaatatctttta-ctccctcctcttcaagtatctac---cccccatgtgcctctgtgcatc--ttggtgggtagcttactggattta----ttttgactttttgttgt--

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA20G23310.4 (Glycine max), 5'ss of exon 5
CTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACTgtaagtatttctca------gcttctttggcattgtgttatgatgtgttcttgtataattttatgaatg----------cataagttagctgtataccatattaa-aacgtattgcatcctcaatgtag----------------------------
 ||||| |||||||| ||||||||||| ||||| ||||||||| | ||||| || ||||| ||||||||| | |||||||| || ||||| ||||| ||||||| ||| | | |       ||  |   | ||         |||||    |||  |  ||  ||  |             ||  ||  || | |    |  ||  |   | |||| |  ||||  | |                            
TTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTATTGATGGAACTgtaaatatcttttactccctcctcttcaagtatctaccccccatgtgcctctgtgcatcttggtgggtagcttactggatttattttgactttttgttgttctattagaatgttgcttgttcaaaattgagttttctatatgctatgcttgacccag

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G43470.1 (Glycine max), 5'ss of exon 5
CTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACTgtaagtatttctca------gcttctttggcattgtgttatgatgtgttcttgtataattttatgaatg----------cataagttagctgtataccat---attaaaacgtattgcatcctcaatgtag--------------------------
 ||||| |||||||| ||||||||||| ||||| ||||||||| | ||||| || ||||| |||||||| || || ||||| || ||||| ||||| ||||||| ||| | |||       ||  |   | ||         |||||    |||  |  ||  ||  |             ||  ||  || | ||   |    ||  || |  |    | |  |||  ||                          
TTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTACCTAACTCTTTCTGCAATTATTGATGGAACTgtaaatatctttcactccctcctcttcaagtatctatcccccatgtgcctctgtgcatcttggtgggtagcttactggatttattttgactttttatagttctgtttgaatggttcttgttcaaaattaagttttatatatgttatgtttgacccag

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 5'ss of exon 5
CTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACTgtaagtatttc---tcagct-tctttggcattg---tgttatgatgtgttcttgtataattttatgaatg-cataagttagctgtataccatattaaaacgtattgcat-cctcaatgtag------------
|||||| || ||||| |||||||| || ||||||||||| ||| | || ||||| |||||||||||||| || || || || || || |||||||| |||||||   | ||   | | || ||| | |||||    |||     |||||   ||| |   | | |   |   |||  | || ||||     |||       | ||  ||  |||| |||              
CTATGATGAGTGCCAGAGGAAGTACGGAAATGCTAATGCATGGCGGTACTGCACAGATGTTTTTGACTACCTAACCCTCTCTGCGATAATAGATGGAACTgtaaacctctcactttatctctctcttgcattaatctgtaccagtgtgtgtgtgtgtgtgtgtgtttttaatatatctaagttgtagtgtctatctgttaatgttatatgtctcattgtttttggaattccag

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 5'ss of exon 5
CTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACTgtaagtatttctcagcttctttggcattgtgttatgatgtgttcttgtataattttatgaatgcataagttagctgtataccatattaaaacgtattgcatcctcaatgtag
 ||||| ||||| ||  | |||||||| ||  | ||||||||| | |||||||| || ||||||||||| || ||||| || ||||| |||||||| |  ||||   |    |     |  |   ||| |||     ||| |  |      |  || |  ||  | |   |    ||| | |  ||      |||  | ||           
TTATGATGAATGTCAGCGTAAGTATGGAAACCCAAATGCTTGGCGGTATTGCACTGACGTTTTTGACTACCTGACACTCTCGGCTATCATAGATGGAAGGgtaaagttcaaacttgcacggttaaattctgtccgtgtgtatgttcaacccagattttcgataaagagcctcttggtagatctcatcgtgctgta--ggatt----------

upper sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 5'ss of exon 5
CTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACTgtaagtatttctcagcttctttggcattgtgttatgatgtgttcttgtataattttatgaatgcataagttagctgtataccatattaaaacgtattgcatcctcaatgtag
 ||||||||||||||  |||||||||| ||  | ||||||||| | || ||||| |||||||||||||| |||||||| ||||| || |||||||| |  |||||        | |||   |||     | ||    ||| |   ||| ||| ||||||  |  | |||  ||      |  | ||   | | |  |  |   | |      
TTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAATAGATGGAAGGgtaaggggg---aaacttacgtggttaaatattgct-tgtatgtctgtttaactttatgttttgagaag--agtctatcagtagatgtcatcatggttgaggatta------

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|125227319|gb|EL241404.1|EL241404
EST:     CACTTTCAGCTATTATAGATGGCACT                         GTTCTATGTGTTCATGGTGGCCTTTCACCTGATGTACGG
genomic: CACTTTCAGCTATTATAGATGGCACTgtaagtattt ... ctcaatgtagGTTCTATGTGTTCATGGTGGCCTTTCACCTGATGTACGG
EST: gi|125001573|gb|EL073842.1|EL073842
EST:     GCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACT                         GTTCTATGTGTTCATGGTGGCCTTTCACCTGATGTACGG
genomic: GCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACTgtaagtattt ... ctcaatgtagGTTCTATGTGTTCATGGTGGCCTTTCACCTGATGTACGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTATAGATGGCACTgtaagtatttctcagcttctttggcattgtgttatgatgtgttcttgtataattttatgaatgcataagttagctgtataccatattaaaacgtattgcatcctcaatgtag

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