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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctatactccaaatcatatccagtttgttattgtatggtgattccttgttttgattacatggattgttaactgaaacattgtatgtctttgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGTGGGAAGATCTACGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGT

Basic information

species Arabidopsis thaliana
transcript AT4G31300.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G31300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 4
-------------------------ttctatactccaaatcatatccagtttg---ttattgtatggtgattccttgttttgattacatgg-attgt-taactgaaacattg--tatgtctttgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGTGGGAAGATCTACGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGT
                         | | | | |   | | |||       ||   |  || | || |  || | |   ||||||  | |  ||||| ||| ||  | ||||  | | ||     |   ||||||||| | ||| ||||  | || ||||| |||||||||||||||||||||||  | || | |    |||| || ||||||||  |  |   |||||| |
gtatattttctgtagcattctacgatacaagaatttcactaatacatgagatgaattctttctctgattctttcatacattgattttaagctattgtctaattgccatattggttttttcaccaattttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGTGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCAT
















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|116424148|gb|EG466740.1|EG466740
EST:     CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAG                         AACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGT
genomic: CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAGgtacaagttt ... tgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGT
EST: gi|86074232|gb|DR369989.1|DR369989
EST:     CTGTTAAGGTTTCTGCTAACCTTATCAGGATGCTCGCATATAATAACAAG                         AACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGT
genomic: CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAGgtacaagttt ... tgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGT
EST: gi|164006253|gb|ES125363.1|ES125363
EST:     CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAG                         AACATGCTCCAAACT
genomic: CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAGgtacaagttt ... tgttgagcagAACATGCTCCAAACT
EST: gi|125208881|gb|EL223835.1|EL223835
EST:     CTTATCAGGATGCTCGCATATAATAACAAG                         AACATGCTCCAAACTGGTCTCATCGTTGGAGGA
genomic: CTTATCAGGATGCTCGCATATAATAACAAGgtacaagttt ... tgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGA
EST: gi|164202645|gb|EL975442.1|EL975442
EST:     GCCAACCTTATCAGGATGCTCGCATATAATAACAAG                         AACATGCTCCAAACTGGTCTCATCGTTGGAGGAT
genomic: GCCAACCTTATCAGGATGCTCGCATATAATAACAAGgtacaagttt ... tgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGAT
EST: gi|164191594|gb|ES130953.1|ES130953
EST:     CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAG                         AACATGCTCCAAACTGGTCTCATCGTTGGAGGATGG
genomic: CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAGgtacaagttt ... tgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGATGG
EST: gi|124974229|gb|EL047803.1|EL047803
EST:     CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAG                         AACATGCTCCAAACTGGTCTCATCGTTGGAGGGTGGGATAAATATGA
genomic: CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAGgtacaagttt ... tgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGA
EST: gi|116444628|gb|EG487220.1|EG487220
EST:     CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAG                         AACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGT
genomic: CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAGgtacaagttt ... tgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGT
EST: gi|164073778|gb|ES099614.1|ES099614
EST:     CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAG                         AACATGCTCCAAACT
genomic: CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAGgtacaagttt ... tgttgagcagAACATGCTCCAAACT
EST: gi|47831542|gb|CK121226.1|CK121226
EST:     CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAG                         AACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGT
genomic: CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAGgtacaagttt ... tgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGT
EST: gi|116444625|gb|EG487217.1|EG487217
EST:     CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAG                         AACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGT
genomic: CTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAGgtacaagttt ... tgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttttgattacatggattgttaactgaaacattgtatgtctttgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGTGGGAAGATCTACGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGT
                    tgttaac  putative branch site (score: 2)
                                         tctttgtt  putative PPT
     tttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctatactccaaatcatatccagtttgttattgtatggtgattccttgttttgattacatggattgttaactgaaacattgtatgtctttgttgagcagAACATGCTCCAAACTGGTCTCATCGTTGGAGGATGGGATAAATATGAGGGTGGGAAGATCTACGGGATCCCACTCGGTGGAACTGTAGTCGAGCAACCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - -ccaaatc
- - - - - - - - - - - agtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaacat