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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTATTGATGCTCTTAAGACCTATGTCCCTGAAATGGTTGAAGTTCTTATTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAGgtagatcattttttttttccttttgtattattctgataactgtgttgaaacttttatgtgacttttagccatgtgtcgatgatcttttccgcag

Basic information

species Arabidopsis thaliana
transcript AT1G51980.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G51980.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g53700.1 (Oryza sativa), 5'ss of exon 3
CACTATTGATGCTCTTAAGACCTATGTCCCTGAAATGGTTGAAGTTCTTATTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAGgtagatcattttttttttccttttgtattattctgataactgtgttgaaacttttatgtgacttttagccatgtgtcgatgatcttttccgcag
 ||   ||||||  | ||| ||||||| ||||| ||||||||||| |||||||| ||||| || ||||| || || ||  |||||||  | || ||  |||||     || | |  ||||     ||  ||| |    | | |||  | |  ||    | | |  ||   |||| | |    |     |  |||
TACCTATGATGCATTCAAGGCCTATGTACCTGAGATGGTTGAAGTGCTTATTGATAGTGTGAGGAACCCAGCCTTTTTTAACTGGGAGATTAAAGAGCAGgta-----ttctgtcattccgaaattagcatttttgatattctgt--atatgttggcatta-taataatgatgtcttg----ttccccctacag

upper sequence: AT1G51980.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 3
CACTATTGATGCTCTTAAGACCTATGTCCCTGAAATGGTTGAAGTTCTTATTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAGgtagatcattttttttttccttttgtattattctgataactgtgttgaaacttttatgtgacttttagccatgtgtcgatgatcttttccgcag
 ||   ||||||  | |||| ||||   || ||||||||||||||||| ||||||||||| || || || || ||| | || ||||| || || ||  |||||  | ||   |         ||| | |  | |        | || |  |||||||||          |   || || |  || ||||  |||
TACCTATGATGCATTGAAGAGCTATACACCAGAAATGGTTGAAGTTCTCATTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatcactgaaaataaattgaagttcttt--------ttttcatccttttatgta---------ctaatggcgttcttcgtttctacag

upper sequence: AT1G51980.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G01720.1 (Glycine max), 5'ss of exon 3
CACTATTGATGCTCTTAAGACCTATGTCCCTGAAATGGTTGAAGTTCTTATTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAGgtagatcattttttttttccttttgtattattctgataactg-tgttgaaacttttatgtgact---tttagccat-gtgtcgatgatcttttccgcag-----
 ||  |||||||  | ||||||||||  ||  ||||||||||| | ||  ||||| |||| || ||||| || |||||||| |||||||| ||||||||||||     || ||||||    ||| | || |       |||| | ||| || | ||| || |      | |  |||  | |   | | ||  |  ||||     
TACATTTGATGCATTAAAGACCTATGCTCCACAAATGGTTGAATTACTGGTTGACTGTGTAAGGAACCCAGCCTTCTTGGATTGGGAAGTCAATGAAGAGgtat----ttattttttcaagtttctcttttctcagggactgatcttgtaattcttaggtcagcaagctcattcatcattttcttcagctaatgggcaggcttt

upper sequence: AT1G51980.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G21380.1 (Glycine max), 5'ss of exon 3
CACTATTGATGCTCTTAAGACCTATGTCCCTGAAATGGTTGAAGTTCTTATTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAGgtagatcattttttttttccttttgtattattctgataactgtgttgaaacttttatgtgacttttagccatgtgtcgatgatcttttccgcag-------------
 ||  |||||||  | ||||||||||| ||  ||||||||||| | ||  ||||| |||| ||  |||| || |||||||| |||||||| ||||||||||||     | ||||||    |||    ||  || |  |    | |||  | | ||| || |     |  |   | ||     | | ||| |||              
TACATTTGATGCCTTAAAGACCTATGTTCCACAAATGGTTGAATTACTGGTTGACTGTGTAAGGCACCCAGCCTTCTTGGATTGGGAAGTCAATGAAGAGgta---tttattttttcaagtttctcttttctccgggactgatcttgtcattcttaggtcagc---aagctcat-tcatcattttcttcagcaactgggctggcttt

upper sequence: AT1G51980.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv09s0002g03200.t01 (Vitis vinifera), 5'ss of exon 3
CACTATTGATGCTCTTAAGACCTATGTCCCTGAAATGGTTGAAGTTCTTATTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAGgtagatcattttttttttccttttgtattattctgataactgtgttgaa-----acttttatgtgacttttagccatgtgtcgatgatcttttccgcag--
|||| |||||||||| ||||| ||||||||||||||||| ||| | ||| ||||| |||| || |||||||  |||||||| |||||||| |||||| ||||| |||  ||   || ||   || ||  ||  | | |     ||  ||     ||||||||     | | ||  |  ||  | | || |||||   |   
CACTTTTGATGCTCTAAAGACTTATGTCCCTGAAATGGTCGAATTGCTTGTTGACTGTGTGAGGAACCCTGTGTTCTTGGATTGGGAAGTCAATGAACAGgtaaatctcttgaattctcaaatt-taccatctttacattaaagtaaaagatgtacttttatccttttataaggaacctgatggttattttttcttgattt

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|164121365|gb|ES093557.1|ES093557
EST:     CTGGGAAGTGAATGAAGAG                         CTACGGAAGATGAAGGTAGTAGATAGCGGAACTTGCAAAGAACCCTATGGG
genomic: CTGGGAAGTGAATGAAGAGgtagatcatt ... ttttccgcagCTACGGAAGATGAAGGTAG-AGATAGCGGAACTTGCAAAGAACCCTATGGG
EST: gi|164182442|gb|ES115959.1|ES115959
EST:     CTGGGAAGTGAATGAAGAG                         CTACGGAAGATGAAGGTAGAGATAGCGGAACTTGCAAAGAACCCTATGGGT
genomic: CTGGGAAGTGAATGAAGAGgtagatcatt ... ttttccgcagCTACGGAAGATGAAGGTAGAGATAGCGGAACTTGCAAAGAACCCTATGGGT
EST: gi|116431222|gb|EG473814.1|EG473814
EST:     TTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAG                         CTACGGAAGATGAAGGTAGAGATAGCGGAACTTGCAAAGAACCCTATGGGT
genomic: TTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAGgtagatcatt ... ttttccgcagCTACGGAAGATGAAGGTAGAGATAGCGGAACTTGCAAAGAACCCTATGGGT
EST: gi|116431237|gb|EG473829.1|EG473829
EST:     TTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAG                         CTACGGAAGATGAAGGTAGAGATAGCGGAACTTGCAAAGAACCCTATGGGT
genomic: TTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAGgtagatcatt ... ttttccgcagCTACGGAAGATGAAGGTAGAGATAGCGGAACTTGCAAAGAACCCTATGGGT
EST: gi|116451725|gb|EG494317.1|EG494317
EST:     TTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAG                         CTACGGAAGATGAAGGTAGAGATA
genomic: TTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAGgtagatcatt ... ttttccgcagCTACGGAAGATGAAGGTAGAGATA
EST: gi|116431221|gb|EG473813.1|EG473813
EST:     TTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAG                         CTACGGAAGATGAAGGTAGAGATAGCGGAACTTGCAAAGAACCCTATGGGT
genomic: TTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAGgtagatcatt ... ttttccgcagCTACGGAAGATGAAGGTAGAGATAGCGGAACTTGCAAAGAACCCTATGGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTATTGATGCTCTTAAGACCTATGTCCCTGAAATGGTTGAAGTTCTTATTGACAGTGTTAGAAACCCTGCTTTCTTGGACTGGGAAGTGAATGAAGAGgtagatcattttttttttccttttgtattattctgataactgtgttgaaacttttatgtgacttttagccatgtgtcgatgatcttttccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA