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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTGTTGGAGGCAACATTATCACTCGTGAAGAGAATGGTTTTCTCTGGGAAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTGgtaagttcttgaaacaatctgattcgttaatactgagaacaatgtatttgtgaattgtttgatttgtggatttagccttctctgtttatggttagagtag

Basic information

species Arabidopsis thaliana
transcript AT4G01690.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G01690.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA02G01000.1 (Glycine max), 5'ss of exon 2
TCGTGTTGGAGGCAACATTATCACTCGTGAAGAGAATGGTTTTCTCTGGGAAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTGgtaagttcttgaaacaatctgattcgttaatactgagaacaatgtatttgtgaattgtttgatttgtggatttagccttctctgtttatggttagagtag--
|   |  || |||||||| | |||    ||       || |  |||||||||||||| ||||| || ||||| || |||||||| |||||||| ||||||||| ||  | |   |  |||      |      ||||   ||      | | ||  ||| |      ||||   |     || | |||   ||   ||    
TGTCGGCGGCGGCAACATCACCACGATGGAGAGTGGCGGATACCTCTGGGAAGAAGGCCCCAACAGCTTTCAGCCCTCTGATCCAATGCTCACCATGGTGgtatgtaat-gtttctttctccaaattcgggtttgagcctaactctactctaaaa-gttagcgcataggataaggttacttccgcttactattttggtcata

upper sequence: AT4G01690.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA10G27890.1 (Glycine max), 5'ss of exon 1
TCGTGTTGGAGGCAACATTATCACTCGTGAAGAGAATGGTTTTCTCTGGGAAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTGgtaagttcttgaaacaatctgattcgttaatactgagaacaa--tgtatttgtgaattgttt--gatttgtggatttagccttctctgtttatggttagagtag
 || || || |||||||| | |||    ||   | | || |  |||||||||||||| ||||| || || || || |||||||| |||||||| ||||||||| ||  | |   |  ||       |   |  ||||   ||  ||    |   | ||  ||  | ||       | |    | | | ||     ||  |    
CCGCGTCGGCGGCAACATCACCACGATGGAGAGGGACGGATACCTCTGGGAAGAAGGCCCCAACAGCTTCCAGCCTTCTGATCCAATGCTCACCATGGTGgtatgtgat-gtttctttcgcggaattcggttttgagcctaacttgaccctaaaagttaattcgggttcaataggtcaattatttgtattatcatttcaaa---
















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|86073723|gb|DR369480.1|DR369480
EST:     AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTG                         GTAGATAGTGGTTTGAAGGATGATTTGGTGTTGGGAGATCCTAC
genomic: AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTGgtaagttctt ... gttagagtagGTAGATAGTGGTTTGAAGGATGATTTGGTGTTGGGAGATCCTAC
EST: gi|86073727|gb|DR369484.1|DR369484
EST:     AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTG                         GTAGATAGTGGTTTG
genomic: AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTGgtaagttctt ... gttagagtagGTAGATAGTGGTTTG
EST: gi|86073725|gb|DR369482.1|DR369482
EST:     AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTG                         GTAGATAGTGATTTGAAGGATGATTT
genomic: AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTGgtaagttctt ... gttagagtagGTAGATAGTGGTTTGAAGGATGATTT
EST: gi|86073726|gb|DR369483.1|DR369483
EST:     AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTG                         GTAGATAGTGGTTAGAAGGATGATT
genomic: AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTGgtaagttctt ... gttagagtagGTAGATAGTGGTTTGAAGGATGATT
EST: gi|86073724|gb|DR369481.1|DR369481
EST:     AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTG                         GTAGATAGTGGTTTGAAGGATGATTTGGTGTTGGGAGATCCTACTGCGCCA
genomic: AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTGgtaagttctt ... gttagagtagGTAGATAGTGGTTTGAAGGATGATTTGGTGTTGGGAGATCCTACTGCGCCA
EST: gi|86073720|gb|DR369477.1|DR369477
EST:     AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTG                         GTAGATAGTGGTTTTGAAGGATGATTTGGTGTTGGGGAGATCCTACTG
genomic: AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTGgtaagttctt ... gttagagtagGTAGATAGTGGTTT-GAAGGATGATTTGGTGTTGGG-AGATCCTACTG
EST: gi|125303301|gb|EL317386.1|EL317386
EST:     AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTG                         GTAGATAGTGGTTTGAAGGATGATTTGGTGTTGGGAGATCCTACTGCGCCA
genomic: AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTGgtaagttctt ... gttagagtagGTAGATAGTGGTTTGAAGGATGATTTGGTGTTGGGAGATCCTACTGCGCCA
EST: gi|86073722|gb|DR369479.1|DR369479
EST:     AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTG                         GTAGATAGTGGTTTGAAGGATGATTTGGTGTTGGGAGATCCTACTGCGCCA
genomic: AAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTGgtaagttctt ... gttagagtagGTAGATAGTGGTTTGAAGGATGATTTGGTGTTGGGAGATCCTACTGCGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTGTTGGAGGCAACATTATCACTCGTGAAGAGAATGGTTTTCTCTGGGAAGAAGGTCCCAATAGTTTTCAACCGTCTGATCCTATGCTCACTATGGTGgtaagttcttgaaacaatctgattcgttaatactgagaacaatgtatttgtgaattgtttgatttgtggatttagccttctctgtttatggttagagtag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG