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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttgatatctttgatttagagacttgtgatagtttctcgcattctgtttgatcagtgtttttcagtatttatagcggttttgtttatttaattggaagGTTCTGAAATGGGAAGATGTGGAAGTAGGGGAACCAAAGGAGGGTGAGATACGTGTGAAGAACAAGGCTATCGGGCTTAACTTTATTGATGTTTACTTCA

Basic information

species Arabidopsis thaliana
transcript AT5G61510.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G61510.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0002g08480.t01 (Vitis vinifera), 3'ss of exon 1
-----actttgatatctttgatttagagacttgtgatagtttctcgcattctgtttgatcagtgtttttcagtatttatagcggttttgtttatttaattggaagGTTCTGAAATGGGAAGATGTGGAAGTAGGGGAACCAAAGGAGGGTGAGATACGTGTGAAGAACAAGGCTATCGGGCTTAACTTTATTGATGTTTACTTCA
     | |    || || | |||| |   |     |||       || | |    | ||   ||    |   || ||||         | | |      ||  |||| ||||| ||||| ||||| ||| |||| || ||||| |||||||||||  ||||||||||| |||| |||||| ||||||| |||||||| |||||| 
ttctgattggagtagctctaattttggagcaccatatatgcatgtgcttccaacattattgttgccaattt-tacttattagaa----gatcaaaatgatgatagGTCCTGAAGTGGGAGGATGTTGAAATAGGAGAGCCAAATGAGGGTGAGATCTGTGTGAAGAACCAGGCCATCGGGGTTAACTTCATTGATGTCTACTTCC
















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|19876022|gb|AU236853.1|AU236853
EST:     AGAAGAAGATGGTGAAAGGGATTAGGGTTTATGAGCATGGCGGTCCTGAN                         GTTCTGAAATGGGAAGATGTGGAAGTAGGGGAACCAAAGGAGGGTGAGATA
genomic: AGAAGAAGATGGTGAAAGGGATTAGGGTTTATGAGCATGGCGGTCCTGAGgtgagtaaaa ... taattggaagGTTCTGAAATGGGAAGATGTGGAAGTAGGGGAACCAAAGGAGGGTGAGATA
EST: gi|164132085|gb|ES014952.1|ES014952
EST:     AGAAGAAGATGGTGAAAGGGATTAGGGTTTATGAGCATGGCGGTCCTGAG                         GTTCTGAAATGGGAAGATGTG
genomic: AGAAGAAGATGGTGAAAGGGATTAGGGTTTATGAGCATGGCGGTCCTGAGgtgagtaaaa ... taattggaagGTTCTGAAATGGGAAGATGTG
EST: gi|125278684|gb|EL292769.1|EL292769
EST:     AGCATGGCGGTCCTGAG                         GTTCTGAAATGGGAAGATGTGGAAGTAGGGGAACCAAAGGAGGGTGAGATA
genomic: AGCATGGCGGTCCTGAGgtgagtaaaa ... taattggaagGTTCTGAAATGGGAAGATGTGGAAGTAGGGGAACCAAAGGAGGGTGAGATA
EST: gi|116455505|gb|EG498097.1|EG498097
EST:     AGAAGAAGATGGTGAAAGGGATTAGGGTTTATGAGCATGGCGGTCCTGAG                         GTTCTGAAATGGGAAGATGTGGAAGTAGGGGAACCAAAGGAGGGTGAGATA
genomic: AGAAGAAGATGGTGAAAGGGATTAGGGTTTATGAGCATGGCGGTCCTGAGgtgagtaaaa ... taattggaagGTTCTGAAATGGGAAGATGTGGAAGTAGGGGAACCAAAGGAGGGTGAGATA
EST: gi|116437739|gb|EG480331.1|EG480331
EST:     AGAAGAAGATGGTGAAAGGGATTAGGGTTTATGAGCATGGCGGTCCTGAG                         GTTCTGAAATGGGAAGATGTGGAAGTAGGGGAACCAAAGGAGGGTGAGATA
genomic: AGAAGAAGATGGTGAAAGGGATTAGGGTTTATGAGCATGGCGGTCCTGAGgtgagtaaaa ... taattggaagGTTCTGAAATGGGAAGATGTGGAAGTAGGGGAACCAAAGGAGGGTGAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttgatcagtgtttttcagtatttatagcggttttgtttatttaattggaagGTTCTGAAATGGGAAGATGTGGAAGTAGGGGAACCAAAGGAGGGTGAGATACGTGTGAAGAACAAGGCTATCGGGCTTAACTTTATTGATGTTTACTTCA
                                          atttaat  putative branch site (score: 4)
                                       tttattt  CT-rich tract
                                  ttttgtttatttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actttgatatctttgatttagagacttgtgatagtttctcgcattctgtttgatcagtgtttttcagtatttatagcggttttgtttatttaattggaagGTTCTGAAATGGGAAGATGTGGAAGTAGGGGAACCAAAGGAGGGTGAGATACGTGTGAAGAACAAGGCTATCGGGCTTAACTTTATTGATGTTTACTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - gatttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttttg