Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttttgctcatttcagctcaaacgaaatcttaattccccaaatgcagaaccaaaaggtttagttcttgatcttcttttgtgtaactttttgcagGATTTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACATTGTCATCACATGTTTCACTTGCCTTGCATAGACAATTGGCTCTTCAGGCACGGATCTTGTC

Basic information

species Arabidopsis thaliana
transcript AT4G35840.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G35840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G36760.1 (Glycine max), 3'ss of exon 5
---gttttttgctcatttcagc-tcaa----acgaaatcttaattcc-----ccaaatgc-----agaaccaaaaggtttagttcttga-----tcttcttttgtgtaactttttgcagGATTTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACATTGTCATCACATGTTTCACTTGCCTTGCATAGACAATTGGCTCTTCAGGCACGGATCTTGTC
     ||||| | | || || | ||||    || | || |  || ||     | |||||      |  |        | |  |   |||     ||| | |||||| ||   | |  |||| |||   ||||| || || || ||||||||||| ||||| ||||||||||||||| | ||||||||||| || ||||||||||| || || ||||| |
gttagtttttacactttacatcgtcaataccactagatgtctataccttgaactaaatgttttctaagattgtgtattgtgatatatgaacatttctgcatttgtgcaa---tatatagGACTTTATGCTTGGAGAGACAGTAAGAAGCTTGCCTCATTGCCATCACATGTTTCACCTACCTTGCATAGATAAGTGGCTCTTCAGACATGGTTCTTGCC

upper sequence: AT4G35840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G08540.1 (Glycine max), 3'ss of exon 4
---gttttttgctcatttcagc-tcaa----acgaaatcttaattccccaaa-tgcagaaccaaaaggtttagt-tcttgatctt--cttttgtgtaactt-----tttgcagGATTTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACATTGTCATCACATGTTTCACTTGCCTTGCATAGACAATTGGCTCTTCAGGCACGGATCTTGTC
     || || | | ||||    ||||    || | || |  || ||   || |  | |     ||| ||  || |  |||| |   | ||| || |  |      | |  |||| |||   ||||| || || || |||||||| || ||||| ||||||||||||||| | ||||||||||| || ||||||||||| || || ||||| |
gttagttcttacacttttctttgtcaataccactagatgtctataccttgaactaaatatttctaagattgtgtattgtgatatgaacatttctgcatttgtgcaatatatagGACTTTATGCTTGGAGAGACAGTAAGAAGCTTACCTCATTGCCATCACATGTTTCACCTACCTTGCATAGATAAGTGGCTCTTCAGACATGGTTCTTGCC

upper sequence: AT4G35840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G05000.1 (Glycine max), 3'ss of exon 4
gttttttgctcatttcagc-tcaaacgaaatcttaattccccaaatgcagaaccaaaaggtttagttcttgatcttcttttgtgtaactt----tttgcagGATTTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACATTGTCATCACATGTTTCACTTGCCTTGCATAGACAATTGGCTCTTCAGGCACGGATCTTGTC
           | ||  |  |   |    || ||| |||      ||   ||  |||     ||    |   | || | ||||| |  ||    ||||||||| ||||| ||||| || || |  ||||| ||||| |||||||||||||| |||||| | |||||||| || || |||||  ||| ||| || ||||| |
-agaaaaaaaaacttaggtatttgattttattttatttctggtggtgataaagaaaagttgctaagcttgtttattttattgtgaatttttgcatttgcagGACTTTCAGCTTGGGGAGACTGGTAGAAGTTTGCCTCATTGTCATCACATTTTTCACCTACCTTGCATTGATAAGTGGCTGATCAAGCATGGTTCTTGCC

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|125112588|gb|EL163650.1|EL163650
EST:     CAAACTTAGATGCTTCTGGCAACAAAGACTCATGTTCTGTTTGTCTTCAG                         GATTTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACATTGTCAT
genomic: C-AACTTAGATGCTTCTGGCAACAAAGACTCATGTTCTGTTTGTCTTCAGgttttttgct ... ctttttgcagGATTTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACATTGTCAT
EST: gi|125219422|gb|EL233507.1|EL233507
EST:     ACAACTTAGATGCTTCTGGCAACAAAGACTCATGTTCTGTTTGTCTTCAG                         GATTTTCAACTTGGTGAAACGGTGAGAAG
genomic: ACAACTTAGATGCTTCTGGCAACAAAGACTCATGTTCTGTTTGTCTTCAGgttttttgct ... ctttttgcagGATTTTCAACTTGGTGAAACGGTGAGAAG
EST: gi|19798828|gb|AU230118.1|AU230118
EST:     ACAACTTAGATGCTTCT-GCAACAAAGACTCATGTTCTGTTTGTCTTCAG                         GATTTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACATTGTCATCACATG
genomic: ACAACTTAGATGCTTCTGGCAACAAAGACTCATGTTCTGTTTGTCTTCAGgttttttgct ... ctttttgcagGATTTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACATTGTCATCACATG
EST: gi|164158454|gb|ES060171.1|ES060171
EST:     GCAACAAAGACTCATGTTCTGTTTGTCTTCAG                         GATCTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACA
genomic: GCAACAAAGACTCATGTTCTGTTTGTCTTCAGgttttttgct ... ctttttgcagGATTTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACA
EST: gi|86084376|gb|DR380135.1|DR380135
EST:     ACAACTTAGATGCTTCTGGCAACAAAGACTCATGTTCTGTTTGTCTTCAG                         GATTTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACATTGTCATCACATG
genomic: ACAACTTAGATGCTTCTGGCAACAAAGACTCATGTTCTGTTTGTCTTCAGgttttttgct ... ctttttgcagGATTTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACATTGTCATCACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgcagaaccaaaaggtttagttcttgatcttcttttgtgtaactttttgcagGATTTTCAACTTGGTGAAACGGTGAGAAGCTTGCCACATTGTCATCACATGTTTCACTTGCCTTGCATAGACAATTGGCTCTTCAGGCACGGATCTTGTC
                                       gtgtaac  putative branch site (score: 3)
                                             ctttttgc  CT-rich tract
                                          taacttttt  TA-rich tract