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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcacttgaattgttatgttttgtgtatgtccgtgctactatatagtttccacttcttgtttgatgttcacaatttgagaaaagccctttctgatttcagCAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCTGGTGCAAGAACTTTGGAACCAAGGACGATTACGAAAAAGAGCATTAAAAGTTTTTTT

Basic information

species Arabidopsis thaliana
transcript AT4G00585.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00585.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0100g01290.t01 (Vitis vinifera), 3'ss of exon 1
---tgcacttgaattgttatgttttgtgtatgtccgtgctact--atatagtttccacttcttgtttgatgttcacaatttgagaaaagccctttctgatttcagCAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCTGGTGCAAGAACTTTGGAACCAAGGACGATTACGAAAAAGAGCATTAAAAGTTTTTTT
      | ||  | | | |          |    ||   ||||  | |||   |  | || |  |  |  |||| ||| |    ||||    |||    || |||||| |||| ||    || || || ||||||||||||||| ||||||||||||| |||||||  |||||  | |              |    | |    |
cacaatatttacaatataagagaagaaaaaaaaacggagtacttaacatatagtgtaattataatgaggagttc-caact----aaaaaatgttttattttgcagCAACGGCCTCATCATCCGGTTCGGCCAATTCCTTCACAGCTCTGGTGCAAGAATTTTGGAAATAAGGAATACTGATTTCTCTGCTGCTGTGTGATAAAAT

upper sequence: AT4G00585.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv15s0046g03680.t01 (Vitis vinifera), 3'ss of exon 2
-tgcacttgaattgttatgttttgtgtatgtccgtgc-tactatatagtttccacttct--tgtttgatgttcacaatttgagaaaagccctttctgatttcagCAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCTGGTGCAAGAACTTTGGAACCAAGGACGATTACGAAAAAGAGCATTAAAAGTTTTTTT
  | | ||      ||    |||   | |||  ||   |  | |    | |  | || |  ||  ||   | || |  ||   | ||    ||  ||    |||||| |||| ||    ||  | || ||||||||||| ||| ||||||||||||| ||||||| ||||||  ||||  |     | || | |     ||   
tcgaattttgtcctttccaattttcatttgtatgtatattatctgcgatatgaatttatgatgactgtgatacagagcttacaagaatattttcttg----cagCAACGGCCTCATCAACCTATTCGTCCAATTCCTTCCCAGCTCTGGTGCAAGAATTTTGGAAACAAGGAGTATTAGAAGCCTCAACAATCATCTAGTTACA
















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|164173882|gb|ES061555.1|ES061555
EST:     TTCCTTGTGTGCATCCCCATCGCCAAGCTATCTGCTAAGCTTGAG                         CAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCTGGTG
genomic: TTCCTTGTGTGCATCCCCATCGCCAAGCTATCTGCTAAGCTTGAGgtatacttca ... ctgatttcagCAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCTGGTG
EST: gi|86019329|gb|DR315075.1|DR315075
EST:     GCGTTTTCCTTGTGKGCATCCCCATCGCCAAGCTATCTGCTAAGCTTGAG                         CAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCT
genomic: GCGTTTTCCTTGTGTGCATCCCCATCGCCAAGCTATCTGCTAAGCTTGAGgtatacttca ... ctgatttcagCAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCT
EST: gi|125163047|gb|EL189817.1|EL189817
EST:     CATCGCCTAGCTATCTGCTAAGCTTGAG                         CAAAGGCCACACATGCCAGTACGCCCAATTCCTTCA
genomic: CATCGCCAAGCTATCTGCTAAGCTTGAGgtatacttca ... ctgatttcagCAAAGGCCACACATGCCAGTACGCCCAATTCCTTCA
EST: gi|125302411|gb|EL316496.1|EL316496
EST:     GCGTTTTCCTTGTGTGCAT-CCCATCGCCAAGCTATCTGCTAAGCTTGAG                         CAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGAT
genomic: GCGTTTTCCTTGTGTGCATCCCCATCGCCAAGCTATCTGCTAAGCTTGAGgtatacttca ... ctgatttcagCAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGAT
EST: gi|86019332|gb|DR315078.1|DR315078
EST:     GCGTTTTCCTTGTGTGCATCCCCATCGCCAAGCTATCTGCTAAGCTTGAG                         CAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCTGGTGCAAG
genomic: GCGTTTTCCTTGTGTGCATCCCCATCGCCAAGCTATCTGCTAAGCTTGAGgtatacttca ... ctgatttcagCAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCTGGTGCAAG
EST: gi|86019335|gb|DR315081.1|DR315081
EST:     GCGTTTTCCTTGTGTGCATCCCCATCGCCAAGCTATCTGCTAAGCTTGAG                         CAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCTGGTGCAAG
genomic: GCGTTTTCCTTGTGTGCATCCCCATCGCCAAGCTATCTGCTAAGCTTGAGgtatacttca ... ctgatttcagCAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCTGGTGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttccacttcttgtttgatgttcacaatttgagaaaagccctttctgatttcagCAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCTGGTGCAAGAACTTTGGAACCAAGGACGATTACGAAAAAGAGCATTAAAAGTTTTTTT
                                           ttctgat  putative branch site (score: 3)
                                       ccctttctgatttc  CT-rich tract
                        acaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcacttgaattgttatgttttgtgtatgtccgtgctactatatagtttccacttcttgtttgatgttcacaatttgagaaaagccctttctgatttcagCAAAGGCCACACATGCCAGTACGCCCAATTCCTTCACAGATCTGGTGCAAGAACTTTGGAACCAAGGACGATTACGAAAAAGAGCATTAAAAGTTTTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaagc