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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttctttttgaattctatgtgtgttaagtgattgttttatggcggtttttagtttgatgggttctttatttttctcttccagTATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACAATGGATGAGATTGTGAAAATGATTGGTTTGAAGAACAATTGCACCTTTT

Basic information

species Arabidopsis thaliana
transcript AT2G44270.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G402242_T01 (Zea mays), 3'ss of exon 3
-----------gtaagc-ttctttttgaattctatgtgtgttaag----tgattgtttta-tg-gcggtttttag-tttgatgggttctttatttttctcttccagTATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACAATGGATGAGATTGTGAAAATGATTGGTTTGAAGAACAATTGCACCTTTT
             |  |   |||  | | || | ||   | |  |    | | | ||||| || | ||| ||| | ||   || |||      ||  ||  | ||||| ||  |||| || ||||||||||| ||||||||| ||||||| |||||||||||||| ||||| |||   |||||| | || |||||||| || || |
gtctcccggtcacagacacacttgctcagttttctggaagctctgactttaaatattttagtgtgtggtatttggattcagtgagtttcactattccctgctgcagTACGGCCTGCCACTGAAGATTGTTTCCTATAAAGATTTGTATGGCTGGACAATGGATGATATTGTCAAAGCAATTGGTCTAAAAAACAATTGTACTTTCT

upper sequence: AT2G44270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 3
--------------gtaagcttctttttgaattctatgtgtgttaagtgattgttttatggcggtttttagtttgatgggttctttatttttctcttccagTATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACAATGGATGAGATTGTGAAAATGATTGGTTTGAAGAACAATTGCACCTTTT
               || |  | | ||| ||  |      ||||   | ||| | | |      || |  ||||  |   || | | ||||| || || |||||||  |||| || ||| |||| || || || ||| ||||||||||||| |||||||| || ||||| ||||| ||||| |||||||| ||||| ||||
aatcttctaaatgtctatgagtatatttcaaagcagaagatgtttctttattttctaaataatattatctgttttttcttttttgtttttttttcctc-agTATGGCCTGCCACTGAAGGTTGTATCTTACAAGGATTTGTATGGATGGACGATGGATGAAATAGTGAAGATGATAGGTTTAAAGAACAACTGCACATTTT
















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|86056680|gb|DR352437.1|DR352437
EST:     CGGGTTATCGTGATGATTCTCTTGAGACTGTTAAACGGAACGAAGTCCAA                         TATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACA
genomic: CGGGTTATCGTGATGATTCTCTTGAGACTGTTAAACGGAACGAAGTCCAAgtaagcttct ... tctcttccagTATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACA
EST: gi|86056681|gb|DR352438.1|DR352438
EST:     CGGGTTATCGTGATGATTCTCTTGAGACTGTTAAACGGAACGAAGTCCAA                         TATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACA
genomic: CGGGTTATCGTGATGATTCTCTTGAGACTGTTAAACGGAACGAAGTCCAAgtaagcttct ... tctcttccagTATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACA
EST: gi|86056682|gb|DR352439.1|DR352439
EST:     CGGGTTATCGTGATGATTCTCTTGAGACTGTTAAACGGAACGAAGTCCAA                         TATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACA
genomic: CGGGTTATCGTGATGATTCTCTTGAGACTGTTAAACGGAACGAAGTCCAAgtaagcttct ... tctcttccagTATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACA
EST: gi|86056679|gb|DR352436.1|DR352436
EST:     CGGGTTATCGTGATGATTCTCTTGAGACTGTTAAACGGAACGAAGTCCAA                         TATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACA
genomic: CGGGTTATCGTGATGATTCTCTTGAGACTGTTAAACGGAACGAAGTCCAAgtaagcttct ... tctcttccagTATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACA
EST: gi|86056683|gb|DR352440.1|DR352440
EST:     CGGGTTATCGTGATGATTCTCTTGAGACTGTTAAACGGAACGAAGTCCAA                         TATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACA
genomic: CGGGTTATCGTGATGATTCTCTTGAGACTGTTAAACGGAACGAAGTCCAAgtaagcttct ... tctcttccagTATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgattgttttatggcggtttttagtttgatgggttctttatttttctcttccagTATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACAATGGATGAGATTGTGAAAATGATTGGTTTGAAGAACAATTGCACCTTTT
                        gtttgat  putative branch site (score: 5)
                                  ttctttatttttctct  putative PPT
                                  ttctttatttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttctttttgaattctatgtgtgttaagtgattgttttatggcggtttttagtttgatgggttctttatttttctcttccagTATGGTTTGCCTCTTAAGATTGTTTCATATAAAGATCTGTATGGATGGACAATGGATGAGATTGTGAAAATGATTGGTTTGAAGAACAATTGCACCTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC