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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttactaccgaaatattcatccagcgctgaagcaatatttgctgatagtttatcataattctgttgttttcagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGTACCAATTGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGAC

Basic information

species Arabidopsis thaliana
transcript AT4G05450.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G05450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g26650.1 (Oryza sativa), 3'ss of exon 3
---------------------gtaagttactaccgaaatattcatccagcgctgaagcaatatttg---ctgatagtttatcataattctgttgttttcagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGTACCAATTGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGAC
                     || | ||        ||  | |||   |   |     |  |||||    |||   |  |  || ||  | |  ||| ||||||| |  | |  |||||||||||||| || |||||||  | |||||||||||| || ||||||||| |||| || || || ||||| ||||| ||||| 
tttttatctgttggctcatgtgtgattt-tggttataaagtccatgttgttttattctacaatttgaacttgaatatcaaatattataatttaatttgcagGATATCTGTGACTTTTGTTGATAAGGATGGCGAGGAAAAGCTTGTTAAAGTACCTATAGGAATGTCAATGCTAGAGGCAGCACATGAGAATGACATAGAA

upper sequence: AT4G05450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0016g00530.t01 (Vitis vinifera), 3'ss of exon 4
----------------gtaagttactac-cgaaatattcatccagcgctgaagcaatatttgctgatagtttatcataattctgttgtttt------cagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGTACCAATTGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGAC
                  | | | ||||      | || |  ||   ||| |   | |||  |     |||| |  | ||||   | |||       ||||||| |  |    |||||||||||||| |||||||||  ||   |||  || || |||||||||||  || | |||||||||||||||||||||||||| 
caatcttagttacacatcatggttctacatttcctcttaactcatttctgcatgtagattaccctggtgtttcttctcattcatatatttaattgtgcagGATATCTGTGTCATTTGTTGATAAGGATGGAGAGGAACATCACATTAGGGTCCCCATTGGAATGTCTATGTTAGAAGCTGCTCATGAAAATGATATAGAA
















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|116443733|gb|EG486325.1|EG486325
EST:     TGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATGAAGAAACTGAGAA                         GATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
genomic: TGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATGAAGAAACTGAGAAgtaagttact ... ttgttttcagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
EST: gi|116443713|gb|EG486305.1|EG486305
EST:     TTCCTCTGAGAATGGTGATGAAGAAACTGAGAA                         GATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
genomic: TTCCTCTGAGAATGGTGATGAAGAAACTGAGAAgtaagttact ... ttgttttcagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
EST: gi|116443730|gb|EG486322.1|EG486322
EST:     TGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATGAAGAAACTGAGAA                         GATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
genomic: TGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATGAAGAAACTGAGAAgtaagttact ... ttgttttcagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
EST: gi|164120929|gb|ES155827.1|ES155827
EST:     GAAACTGAGAA                         GATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
genomic: GAAACTGAGAAgtaagttact ... ttgttttcagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
EST: gi|116443725|gb|EG486317.1|EG486317
EST:     TGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATGAAGAAACTGAGAA                         GATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
genomic: TGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATGAAGAAACTGAGAAgtaagttact ... ttgttttcagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
EST: gi|116443734|gb|EG486326.1|EG486326
EST:     TGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATGAAGAAACTGAGAA                         GATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
genomic: TGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATGAAGAAACTGAGAAgtaagttact ... ttgttttcagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
EST: gi|116443712|gb|EG486304.1|EG486304
EST:     TGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATGAAGAAACTGAGAA                         GATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
genomic: TGTACTTCTTCAACAACTTCCTCTGAGAATGGTGATGAAGAAACTGAGAAgtaagttact ... ttgttttcagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
EST: gi|86076925|gb|DR372682.1|DR372682
EST:     GTGATGAAG-AACTGAGAA                         GATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT
genomic: GTGATGAAGAAACTGAGAAgtaagttact ... ttgttttcagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccagcgctgaagcaatatttgctgatagtttatcataattctgttgttttcagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGTACCAATTGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGAC
                     tgctgat  putative branch site (score: 3)
                                             ttgttttc  putative PPT
                          atagtttatcataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttactaccgaaatattcatccagcgctgaagcaatatttgctgatagtttatcataattctgttgttttcagGATAACCATAATCTTTGTTGATAAGGACGGAGAGGAAATTCCTGTTAAAGTACCAATTGGAATGTCAGTGCTCGAAGCTGCTCATGAAAATGATATAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT