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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAGgtatgtttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtggaaaatcattattcag

Basic information

species Arabidopsis thaliana
transcript AT4G02480.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 5'ss of exon 23
TGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAGgtatgt---ttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtggaaaatcattattcag
||||||||||| ||||||||||  || |||||||| || ||  | || ||||| ||||| |||||||| ||||| || ||||||||| ||   ||| |  |  | ||   |     || ||||      ||| ||| |   |  || |  | ||  ||||  ||||  || ||||  |              
TGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGgtaagtaaattgtaattgatcaatcacaacgcct-ttctgaattccctgtgatgtttgctttctagtttatcttcttcatcttgtg-ttgtatag-------------

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 5'ss of exon 23
TGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAGgtatgtttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtggaaaatcat-tattcag
|||||||| ||||| ||||| || || |||||||| || ||  | || ||||| ||||| || |||||||||||||| ||||||||  ||    | |  |   |  |   | | | ||       |   |||  |   | |      | ||  ||  | || |     || ||||  | ||| ||     
TGGTTTGGCGAGGGTGAGAAATATGTCAAAGCTGTGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAGgtcagtcaacaaaattcttatggtcattttttttggaatgaa---ttgtcgtttggcccaccttttatattaccaatgtttcagtt-tggaccaccatatacct--

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 22
TGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAGgtatgtttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtggaaaatcat--tattcag--
||||||||||| ||||||||||| || ||||||||||| ||  |||| ||||| ||||| |||||||| ||||||||||| ||||| || || |  || | |        | | | |||  |   |  | |     |  |  |||||  || | | |     | ||  || |   || ||||   |  ||   
TGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAGgt-tgctttatcatgtcatttg----tttatattcctttgaagttctcttttcctttattttaaatattatttt----taatactttttagaattcatatgagccattt

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: GLYMA02G17410.1 (Glycine max), 5'ss of exon 18
TGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAGgtatgtttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctc--gatctgatgattgtggaaaatcattattcag
||||||||||| |||||||| || || ||||| ||||| ||  | || ||||| ||||| |||||||| ||||||||||| ||||| || || |  || | |        | | | |||  |   |  |||     |  |  |||||  || ||| |    | ||  | |   |  | |      |||   
TGGTTTGGTGAAGGAGAGAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAGgt-tgctttattatgtcatttg----tttatcttcctttgaatttttcttttcctttattttaaatattttttttaaaactttttacccttcatatgagccattt--

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 19
TGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAGgtatgtttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtggaaaatcattattcag
||||||||||| ||||| || || || ||||| ||||| ||  | || ||||| ||||| |||||||| |||||||||||||||||  || |    |||  | | | | | || | || |||      |    |  |    ||| | |  | |||  |  | | || ||  |  |      || |    
TGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAGgttggtat----ataacatatatcttccttttttttcttggttttaaatattctaaatttctttacattttgaccgttttataat-atccatttgtgttgtcgga

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 22
lower sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 19
TGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAGgtatgtttgaagatattaaaaagcgttctctgttctctcccacctttga-agccagtctttttatgtactttctcgatctgatgattgtggaaaatcattattcag--
||||||||||| ||||| || || || ||||| ||||| ||  | || ||||| ||||| |||||||| |||||||||||||||||  ||      |||  | | | | | || | || |        ||  | |  |    ||| | |  | |||  |  | | || || ||  |      || | |||  
TGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAGgttggt------ataacatatatcttccttttttttactttgttttaaatattctaaatttctttacattttgaccgttttataat-gtccatttgtgttgt-cagtt

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|124734802|gb|EH826204.1|EH826204
EST:     AGTGTCATTTTTGTTGATGAG                         GTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATG
genomic: AGTGTCATTTTTGTTGATGAGgtatgtttga ... cattattcagGTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATG
EST: gi|86063353|gb|DR359110.1|DR359110
EST:     TCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAG                         GTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATG
genomic: TCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAGgtatgtttga ... cattattcagGTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATG
EST: gi|86063355|gb|DR359112.1|DR359112
EST:     TCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAG                         GTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATG
genomic: TCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAGgtatgtttga ... cattattcagGTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTCTTCTCCTTAGCGAGCAAGATTGCGCCAAGTGTCATTTTTGTTGATGAGgtatgtttgaagatattaaaaagcgttctctgttctctcccacctttgaagccagtctttttatgtactttctcgatctgatgattgtggaaaatcattattcag

- - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA