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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTCAACATTGAGAAACTCCAGCTTGTTGAGGCGGAGAAGAAGAAGATCAGGCAAGATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGATgtgagttttctgatttcaatttttttgatcttggttaagttttaagttagatcgcttgttctggattacaatatctctgaactttgaaaaaattagaagt...

Basic information

species Arabidopsis thaliana
transcript AT4G11150.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G11150.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv02s0025g01000.t01 (Vitis vinifera), 5'ss of exon 2
AATTCAACATTGAGAAACTCCAGCTTGTTGAGGCGGAGAAGAAGAAGATCAGGCAAGATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGATgtgagttttctgatttcaatttttttgatcttggttaagttttaagttagatcgcttgttctggattacaatatctctgaactttga---aaaaattagaagt--
||||||||||||||||  | ||||||||||| |||||||||||||||||||| || || ||||||   || |||||||||| |||| |||| ||||| |||| | ||     | |   || |  ||||| |   |    ||||  ||  |||| | |  |  | |||    | |   | | || | |   |   |||     |  
AATTCAACATTGAGAAGTTGCAGCTTGTTGAAGCGGAGAAGAAGAAGATCAGACAGGAATATGAGCGAAAAGAGAAGCAAGTTGATATTCGGAAGAAAATgtaaattactgaact---atgtacttgatttctttggcatttttggt--gatcacattgtgagaattggtttgttgttaagctctaagctatggatttctgatca
















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|164090193|gb|ES176541.1|ES176541
EST:     GGCAAGATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGAT                         TGATTACTCTATGCAGCTAAATGCATCAAG
genomic: GGCAAGATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGATgtgagttttc ... gttttttcagTGATTACTCTATGCAGCTAAATGCATCAAG
EST: gi|164191611|gb|ES132174.1|ES132174
EST:     AGGCAAGATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGAT                         TGATTACTCTATGCAGCTAAATGCATCAAG
genomic: AGGCAAGATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGATgtgagttttc ... gttttttcagTGATTACTCTATGCAGCTAAATGCATCAAG
EST: gi|125287818|gb|EL301903.1|EL301903
EST:     ATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGAT                         TGATTACTCTATGCAGCTAAATGCATCAAGGATCAAAGTTCTTCA
genomic: ATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGATgtgagttttc ... gttttttcagTGATTACTCTATGCAGCTAAATGCATCAAGGATCAAAGTTCTTCA
EST: gi|125256061|gb|EL270146.1|EL270146
EST:     CAAGATTATGTGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGAT                         TGATTACTCTATGCAGCTAAATGCATCAAGGATCAAA
genomic: CAAGATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGATgtgagttttc ... gttttttcagTGATTACTCTATGCAGCTAAATGCATCAAGGATCAAA
EST: gi|125080460|gb|EL142049.1|EL142049
EST:     CAAGATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGAT                         TGATTACTCTATGCAGCTAAATGCATCAAGGAT
genomic: CAAGATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGATgtgagttttc ... gttttttcagTGATTACTCTATGCAGCTAAATGCATCAAGGAT
EST: gi|164073867|gb|ES209757.1|ES209757
EST:     GGCAAGATTATGAGAAGAAGGAGAAGCAACGCTGATGTTCGCAAGAAGAT                         TGATTACTCTATGCAGCTAAATGCATCAAGGAT
genomic: GGCAAGATTATGAGAAGAAGGAGAAGCAA-GCTGATGTTCGCAAGAAGATgtgagttttc ... gttttttcagTGATTACTCTATGCAGCTAAATGCATCAAGGAT
EST: gi|86072192|gb|DR367949.1|DR367949
EST:     AGGCNAGATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGAT                         TGATTACTCTATGCAGCTAAATGCATCAAGGATCAAAGTTCTTCAAGCGCA
genomic: AGGCAAGATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGATgtgagttttc ... gttttttcagTGATTACTCTATGCAGCTAAATGCATCAAGGATCAAAGTTCTTCAAGCGCA
EST: gi|125256905|gb|EL270990.1|EL270990
EST:     GATGTTCGCAAGAAGAT                         TGATTACTCTATGCAGCTAAATGCATCAAGGATCAAAGTT
genomic: GATGTTCGCAAGAAGATgtgagttttc ... gttttttcagTGATTACTCTATGCAGCTAAATGCATCAAGGATCAAAGTT
EST: gi|125192711|gb|EL207665.1|EL207665
EST:     CAAGCTGATGTTCGCAAGAAGAT                         TGATTACTCTATGCAGCTAAATGCATCAAGGATCAAAGTT
genomic: CAAGCTGATGTTCGCAAGAAGATgtgagttttc ... gttttttcagTGATTACTCTATGCAGCTAAATGCATCAAGGATCAAAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTCAACATTGAGAAACTCCAGCTTGTTGAGGCGGAGAAGAAGAAGATCAGGCAAGATTATGAGAAGAAGGAGAAGCAAGCTGATGTTCGCAAGAAGATgtgagttttctgatttcaatttttttgatcttggttaagttttaagttagatcgcttgttctggattacaatatctctgaactttgaaaaaattagaagt

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat