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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattttcgctagtacatgggtgatttttttaagcatcttactttctcttttgcaaggtctaatatttttatatgccattgtag

Basic information

species Arabidopsis thaliana
transcript AT5G22330.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 5'ss of exon 6
TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgt-----gattttcgctagtacatgggtgatttttttaagc--------atcttactttctcttt--------tgcaaggtctaatatttttatatgccattgtag---
|| ||| ||||| ||||| |||||  | ||  | ||||| ||||||||||| || || |||||||| |||||||| ||||||||||||||||| || |||||       |||  | | |  |       ||| ||| || |        || | |    |  |          || | | |||   || |||||||  |||| |||   
TCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTGAAATCACTGACAAGCTTCGGCAAGAAATCAATAAGgtttttcagtttctgattgagcggcacccattctttgaaactggattaaatttaatgaacattccaggatcgatgtatgatctttaatctttatattgcattttagtag

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G018697_T03 (Zea mays), 5'ss of exon 7
TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattttcgctagtacatgggtgatttttttaagcatcttac----tttctcttttgcaaggtctaata----tttttatatgccattgtag---------------
||  || ||||||||||| |||||  | ||  | |||||||| ||||||||||| || |||||||| ||||| || || || || ||||||||||| |||||  | |||  |   ||       |||||||| ||  |||||     | ||   |||| |    |  |||    |||| |  ||   ||  |                
TCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTGAAATCACCGAAAAACTACGCCAAGAAATTAATAAGgttttcttctttttgact---accattttttttagtttcttaggcagtatcaaatttggataaccatataagaattttcagctggtttttaattttatatgatgacag

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 6
TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGg---tgattttcgct---agt--acatgggtgatttttttaagca-tcttactttctcttttgcaaggtctaatatttttatatgccattgtag---------------
 |  || ||||||||||| |||||  | ||  | |||||||| |||||||| || ||||||||||| ||||| || ||||| || |||||||| || ||||   |||||||   |   ||   || |   | | |||| || ||| | | |  || | | |    | ||   | || || |  ||   ||  |                
CCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTGAAATCACCGAAAAGCTACGCCAAGAAATCAATAAGgttttgattttttttttcagctaactttttttagttttataggcagtatcaaattttatataatcatgtaaga-atcttcacctgattttaaattttacatggtgaaag

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 6
TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattttcgctagtacatgggtgatttttttaag-catcttactttctcttttgcaaggtctaatatttttatatgccattgtag---------------
 ||||||||||| || || ||||| || ||| | ||||| || |||||||| ||  |||| || ||||||||||| ||| |  ||||||||||||||||||| ||||||   | |         | ||| |     ||||||   ||   | | |  |    |||   | | | |    |   |                 
ACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAGAGATCACTGACAAGTTGAGGCAAGAAATTAACAAGgt-attttcataacttttgatacaagtttgtagtttcatctttaattagttatggggaaaattaagggtctaaaaaatgagcttttttcttagcaatttct

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G21830.1 (Glycine max), 5'ss of exon 6
TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattt-----tcgctagtacatgggtg-atttttttaagcatcttactttctcttttgcaaggtctaatatttttatatgccattgtag---------
 ||||||||||| || || ||||| || ||| ||||||| || |||||||| ||  |||| || || |||||||| ||| |  ||||||| |||||||||||  |||         |  |||| |  || | ||| |||   ||   |     |      | |    | |  ||||    |  || | |           
ACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAGAAATCACTGACAAGTTGAGGCAAGAGATTAACAAGgtattttaataacttttgatacaagtttgtagtttcttatttatgggaaaaattaagggtcgaaaagtgagcttttgtcttagcaatttgttcaattgct

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 5'ss of exon 7
TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattttcgctagtac------atgggtgatttttttaagcatcttactttctctt-ttgcaaggtc-taatattt-ttatatgccattgtag---------------------------------------------------
||| |||||||| ||||| |||||| | ||  |||||||||| ||||||||||| || |||||||| || ||||||||  | || ||||| ||||||||||| |||||   |    |       || ||         || | || |||    || | ||| ||  |  || ||||  | |   |  | ||  |                                                   
TCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTGAAATTACTGATAAATTACGACAAGAGATTAACAAGgtaatttttcttgacgctgtgctgtgagtatggacaagaaacctcgtacaaagtcgtgttgtaacattatattattaatcaagaggtaatgctgagtcagaagggcaacgagtttgagatggtttctcgttcatttgtggtgcag

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S40_80V6.1 (Physcomitrella patens), 5'ss of exon 1
TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtg-----attttcgcta----------gtacatgggtgatttttttaagcatcttactttct--cttttgcaaggtctaatatttt-tatatgccattgtag--------------------------------------------------------------------
                          | ||  | ||| |||| ||||||||||| |  |||||||| || |||||||||||  | |||||||||||||||||       |||| | |           ||  ||| |   | || |  |  ||  |  | | |    ||   |  ||| || |  |  |||||     | ||                                                                     
-------------------------ATGTCCATAATGAGCCAGATGATGAAACCTCACAAGACTGAAATTACTGATAAGCTAAGTCAAGAAATTAACAAGgtataaatgtttttggtctcaactccatgtgaatgtggagtcttgtacaatatagtgttgtttgatcttcatattgtcaaacaagtgatatatatatatatatatatatatatatctagcaaggagagttacaggttagggctaataatttcttattcatccactgtgcag

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ33466 (Selaginella moellendorffii), 5'ss of exon 6
TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattttcgctagtacatgggtgatttt--tttaagcatcttactttctcttttgcaaggtctaatatttttatatgccattgtag
 || ||||||||||| || ||||| |||||  ||||||| || |||||||| |||   ||||||||||||||||||||||| ||||| ||||| |||||||| |    |    || | |  |   |  |  ||  || || ||   || |||   | |   | |      | | | || ||      
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAGCTGCGGCAGGAAATCAACAAGgttagcagccggcgttcgtcagctctcctgtttcgaggattttctattgtctaaaggattatgtgtggcatgtttgtggcag-----

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ27201 (Selaginella moellendorffii), 5'ss of exon 6
TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattttcgctagtacatgggtgattt-ttttaagcatcttactttctcttttgcaaggtctaatatttttatatgccattgtag
 || ||||||||||| || ||||| |||||  ||||||| || |||||||| |||   |||||||||||||||||||| || ||||||||||| |||||||| |    || |  |     | |    | |||| || || ||   || |||   | |   | |      | | | || ||      
GCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTGAGATCACTGATAAACTACGGCAAGAAATCAACAAGgttagc--cggtgttcgtcagctctcctgttttgaggattttctattgtctagaggattatgtgtgggatctttgtggcag-----

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|116443983|gb|EG486575.1|EG486575
EST:     AACCGCGGA-GACTGAGATCACTGATA-GCT-CGGCA-GAAATTAACA-G                         GT-GTGA-CCGATATAT
genomic: AACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattttcg ... gccattgtagGTTGTGAACCGATATAT
EST: gi|116443984|gb|EG486576.1|EG486576
EST:     TAAGCTTCGGCAAGAAATTAACAAG                         GTTGTGAACCGATATATAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTT
genomic: TAAGCTTCGGCAAGAAATTAACAAGgtgattttcg ... gccattgtagGTTGTGAACCGATATATAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTT
EST: gi|164204488|gb|ES031821.1|ES031821
EST:     AACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAG                         GTTGTGAACCGATATATAG
genomic: AACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattttcg ... gccattgtagGTTGTGAACCGATATATAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTGAGATCACTGATAAGCTTCGGCAAGAAATTAACAAGgtgattttcgctagtacatgggtgatttttttaagcatcttactttctcttttgcaaggtctaatatttttatatgccattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA