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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGATCGCCAATGGAATGCTAAGGTTTCGGATTTTGGACTTGCTAAGCTCTTGGGGTCTGAGAGCAGTTATGTGACTACTCGTGTGATGGGAACTTTCGGgtaaactattaaactcattaactctctcctgcaatctgcaaggcagtctttaggaatgtgaatattaggaaataacttttactttgtgggttgatttgtttag

Basic information

species Arabidopsis thaliana
transcript AT1G01540.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os03g03410.1 (Oryza sativa), 5'ss of exon 4
TTGATCGCCAATGGAATGCTAAGGTTTCGGATTTTGGACTTGCTAAGCTCTTGGGGTCTGAGAGCAGTTATGTGACTACTCGTGTGATGGGAACTTTCGGgtaaactattaaactcattaactctct-cctgcaatctgcaaggcagtctttaggaatgtgaatattaggaaataacttttactttgtgggttgatttgtttag
|||| |  |||||||||||||| || || |||||||| ||||| ||||| ||| | || ||||| |||||||| ||||| ||||| |||||||| || |||| |  |||| |    ||  || | |  |||  | | | ||    |||   ||    |    ||    | || |  ||   |  |||  |              
TTGACCAGCAATGGAATGCTAAAGTGTCAGATTTTGGTCTTGCGAAGCTATTGTGCTCAGAGAGAAGTTATGTTACTACCCGTGTTATGGGAACCTTTGGgttag-tattga--caatccacacacaacctttactgtacataaaagttagtacatcttatcatgactgaaattggct---atgttgcag--------------

upper sequence: AT1G01540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA09G39160.1 (Glycine max), 5'ss of exon 4
TTGATCGCCAATGGAATGCTAAGGTTTCGGATTTTGGACTTGCTAAGCTCTTGGGGTCTGAGAGCAGTTATGTGACTACTCGTGTGATGGGAACTTTCGGgtaa--actattaaact---cattaac---tctctcctgc-aatctgcaagg----cagtctttaggaatgtgaatattaggaaataacttttact--ttgtgggttgatttgtttag---------------------------
||||||||||||||||  | |||||||| |||||||||||||||||||| ||| | |||||||  ||||| || || ||||| |||||||| || || |||| |  |  ||||| ||   ||||  |   |||||| | | ||  |  ||      ||   |   | |   |    ||  | || |      || |  ||   |||  |    | | |                           
TTGATCGCCAATGGAACTCCAAGGTTTCCGATTTTGGACTTGCTAAGCTTTTGTGTTCTGAGAATAGTTACGTCACAACTCGAGTGATGGGGACATTTGGgttagtatgattaagctaagcattctcctatctctcttaccaaattataattagttcaagttcctgtatgattgcaatgtgtaagtggtccctaatgtttaaaggtcaaaagatattgattctctccttttttctttttctgtag

upper sequence: AT1G01540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA18G47170.1 (Glycine max), 5'ss of exon 4
TTGATCGCCAATGGAATGCTAAGGTTTCGGATTTTGGACTTGCTAAGCTCTTGGGGTCTGAGAGCAGTTATGTGACTACTCGTGTGATGGGAACTTTCGGgtaa--actattaaactca--------ttaactctctcctgcaatctgcaaggcagtctttag---gaatgtgaatattagg---aaataactttta--ctttgtgggttgatttgtttag---------------------------
 |||||||||||||||  | |||||||| |||||||| ||||||||||| ||  | |||||||  |||||||| || ||||| ||||||||||| || |||| |  |  ||||| || |         || ||||||| | | |  |   |   ||| || ||      | ||| |   | |   || |   |   |   |||   |||  | |  | | |                           
-TGATCGCCAATGGAACTCCAAGGTTTCTGATTTTGGGCTTGCTAAGCTTTTATGTTCTGAGAATAGTTATGTCACAACTCGAGTGATGGGAACATTTGGGttagtatgattaagctaagcattatcctatctctctcttaccaaattataattagttttaagttcctgtatgattgcaatgtgtaagtggttccaaatttttaaaggtaaaatgatattgattctctcctttttctttttctgtagt

upper sequence: AT1G01540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA16G03650.1 (Glycine max), 5'ss of exon 4
TTGATCGCCAATGGAATGCTAAGGTTTCGGATTTTGGACTTGCTAAGCTCTTGGGGTCTGAGAGCAGTTATGTGACTACTCGTGTGATGGGAACTTTCGGgtaa--actattaaactcattaact------ctctcctgcaatctgcaag-----gcagt--ctttaggaatgtgaatattaggaaataacttttactttgtgggttgatttgtttag-------------------------------
||||||||||||||||  | |||||||| |||||||| ||||||||||| |||    ||||    |||||||| |||||||| |||||||| || || |||| |  |   || |||| |  |  |      || |  ||| |  |  ||       || |  || || ||     |    |    | | | | ||||| |     || |  |    ||                               
TTGATCGCCAATGGAACCCAAAGGTTTCTGATTTTGGGCTTGCTAAGCTTTTGTCAGCTGATCATAGTTATGTCACTACTCGAGTGATGGGGACATTTGGgttagtatggtttaactaagcattttcctagctttgttgccaattataattagtttcaatacctgtaagagcaaaatgtgttattagtcattcttactctcaaatttaaagtccacagtactgattctctcccctttctttttctgcag

upper sequence: AT1G01540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA07G07250.1 (Glycine max), 5'ss of exon 5
TTGATCGCCAATGGAATGCTAAGGTTTCGGATTTTGGACTTGCTAAGCTCTTGGGGTCTGAGAGCAGTTATGTGACTACTCGTGTGATGGGAACTTTCGGgtaa--actattaaact---cattaac---tctctcctgcaatctgcaag-----gcagtctttaggaatgtgaa------tattaggaaataacttttac---tttgtgg-gttgatttgtttag-----------------------
|||||||||| |||||  | |||||||| |||||||| ||||||||||| |||    | ||    |||||||| |||||||| |||||||| || || |||| |  |   || ||||   ||||  |   ||| |  ||| |  |  ||       ||||  ||   |  |  ||      ||||||  | ||   ||  |   ||| |||   | | |  ||                          
TTGATCGCCAGTGGAACCCAAAGGTTTCTGATTTTGGGCTTGCTAAGCTTTTGTCAGCGGATCATAGTTATGTCACTACTCGAGTGATGGGGACATTTGGgttagtatggtttaactaagcattttcctatctttattgccaattataattaatttcagtacttgtaagagcaaaatgtgttattagttattattattctcaaatttatggtactcactcattggttttctccctttctctttctgcag

upper sequence: AT1G01540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 5'ss of exon 4
TTGATCGCCAATGGAATGCTAAGGTTTCGGATTTTGGACTTGCTAAGCTCTTGGGGTCTGAGAGCAGTTATGTGACTACTCGTGTGATGGGAACTTTCGGgtaaactattaaactcattaactctctcctgcaatctgcaaggcagtctttaggaatgtgaatattaggaaataacttttactttgtgggttgatttgtttag
||||||||||||||||  ||||||| || |||||||| || || ||||||||  | |||||||  |||||||| || ||||||||||||||||| ||||||| |           ||||   ||  |   | |||      | |  ||      |||| | |||||  |||  |  | | |  ||      ||  || |  ||
TTGATCGCCAATGGAACTCTAAGGTGTCTGATTTTGGGCTGGCAAAGCTCTTATGTTCTGAGATAAGTTATGTAACGACTCGTGTGATGGGAACATTCGGgttag--------tccatt---tccttttggtaatgaatc-gaccttcacataaaatg-gcatattgagaag-atttctgatatttcccaatggctt-tccag

upper sequence: AT1G01540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S358_6V6.1 (Physcomitrella patens), 5'ss of exon 4
TTGATCGCCAATGGAATGCTAAGGTTTCGGATTTTGGACTTGCTAAGCTCTTGGGGTCTGAGAGCAGTTATGTGACTACTCGTGTGATGGGAACTTTCGGgtaaactattaaactcattaactctctc-ctgcaatctgcaaggcagtctttaggaatg-tgaatattaggaaataacttttactttgtgggttgatttgtttag----------------
| |||   ||||||||||||||||| || |||||||||||||| |||||  | || ||||  |  ||  |||| || || ||||| |||||||||||||||||| |    |   | ||| | |  |||  || ||     |  ||||     |    ||   | |||| |    |   |  |  |||     |||| | |||  |                
TGGATGCGCAATGGAATGCTAAGGTGTCTGATTTTGGACTTGCCAAGCTTCTTGGCTCTGGCAAGAGCCATGTCACCACGCGTGTCATGGGAACTTTCGGgtaagcgtaaagtatgatttattgcctcgttgtaacaataattgcagctagcaacggtgacaagtatttgtttgtctttcatggttttctccttgagtcgttacgatggttgtttttgcag

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|124995954|gb|EL068223.1|EL068223
EST:     TTGGGGTCTGAGAGCAGTTATGTGACTACTCGTGTGATGGGAACTT-CGG                         TTATGTAGCACCAGAATACGCTTGCACCGGAATG
genomic: TTGGGGTCTGAGAGCAGTTATGTGACTACTCGTGTGATGGGAACTTTCGGgtaaactatt ... atttgtttagTTATGTAGCACCAGAATACGCTTGCACCGGAATG
EST: gi|125178491|gb|EL196904.1|EL196904
EST:     CTCGTGTGATGGGAACTTTCGG                         TTATGTAGCACCAGAATACGCTTGCACCGGAATGTTAAACGAGAAGAGTGA
genomic: CTCGTGTGATGGGAACTTTCGGgtaaactatt ... atttgtttagTTATGTAGCACCAGAATACGCTTGCACCGGAATGTTAAACGAGAAGAGTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGATCGCCAATGGAATGCTAAGGTTTCGGATTTTGGACTTGCTAAGCTCTTGGGGTCTGAGAGCAGTTATGTGACTACTCGTGTGATGGGAACTTTCGGgtaaactattaaactcattaactctctcctgcaatctgcaaggcagtctttaggaatgtgaatattaggaaataacttttactttgtgggttgatttgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG