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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatcattgtctttcatttatgattataatgtgtataagcaattgtggttgttatttatgtgttgctgtgtttggcttttggttttagATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCGAGTAACAAGCGGAAGATCATCTGTGATGATGCGTTGCGTGTGGTTTTTG

Basic information

species Arabidopsis thaliana
transcript AT4G22360.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G22360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G43590.2 (Glycine max), 3'ss of exon 2
---gttatcattgtctttca---tttatgattataatgtgtataagca-attgtggttgttatttatgtgtt---gctgtgtttggcttttggttttagATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCGAGTAACAAGCGGAAGATCATCTGTGATGATGCGTTGCGTGTGGTTTTTG
     || |  | | ||| |   ||  || ||      || ||||      | | |||   |   |  | |      ||||       | |||||||||||||||| |||| |||||||||| ||||||||||| || || ||||| || || |||||  |||| || || ||  ||||||   |||||||||| ||||
gtttgtaccgatatttttgaagcttgttgtttgcttaatgcataattttgatatagtttccagcgagatttctaaaatgtggagtaactgtggttttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCCAGCAACAAAAGGAAAATAATTTGCAATGATGAACTGCGTGTGGTGTTTG

upper sequence: AT4G22360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0187g00190.t01 (Vitis vinifera), 3'ss of exon 2
------------------gttatcattgtcttt--catttatgattataatgtgtat--aagcaattgtggttgttatttatgtgttgct-gtgtttggcttt--tggttttagATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCGAGTAACAAGCGGAAGATCATCTGTGATGATGCGTTGCGTGTGGTTTTTG
                   | | | || |||||  ||       |||| | || |    ||| | || | |    | || | ||    || |   |   | ||  | | || ||||||||| |||  | ||||| || || ||||| || ||||| ||||| || ||||||||||| ||||| || |||||||||||  | ||  |||| ||||
gttcttattctcatagaaatgaactttctctttatcaggctcacttatcaggttttgtgaagtagttatagaatatcttgaagtaacccttgaactccaccttgcttggttcagATTGTGAAGCAGCTTTGGGCATACATTAGGAAAAACAACCTCCAAGATCCTAGTAACAAGCGAAAGATAATTTGTGATGATGCCCTCCGCTTGGTGTTTG

upper sequence: AT4G22360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0187g00240.t01 (Vitis vinifera), 3'ss of exon 2
----------------------gttatcattgtctttcattta-tgattataatgtgtataagcaattgtggttgttatttatgtgttgct-gtgtttggcttt--tggttttagATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCGAGTAACAAGCGGAAGATCATCTGTGATGATGCGTTGCGTGTGGTTTTTG
                        | ||  | | |     | | | || |   | |||  ||| | || | |    | || | ||    || |   |   | ||  | | || ||||||||| |||  | ||||| || || ||||| || ||||| ||||| || ||||||||||| ||||| || |||||||||||  | ||  |||| || |
gttcttattctcatagaaatgaactttctctatatcaggctcacttatcaggttttgtg-aagtagttatagaatatcttgaagtaacccttgaactccaccttgcttggttcagATTGTGAAGCAGCTTTGGGCATACATTAGGAAAAACAACCTCCAAGATCCTAGTAACAAGCGAAAGATAATTTGTGATGATGCCCTCCGCTTGGTGTTCG

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|47830511|gb|CK120195.1|CK120195
EST:     CTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTTCCTAGAACTGAG                         ATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCG
genomic: CTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTTCCTAGAACTGAGgttatcattg ... ttggttttagATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCG
EST: gi|124892614|gb|EH971516.1|EH971516
EST:     CTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTTCCTAGAACTGAG                         ATTGTGAGGCAATT
genomic: CTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTTCCTAGAACTGAGgttatcattg ... ttggttttagATTGTGAGGCAATT
EST: gi|124888336|gb|EH967238.1|EH967238
EST:     GAAGTAGTTGTTGGTG-ACCTGCTCTTCCTAGAACTGAG                         ATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAA
genomic: GAAGTAGTTGTTGGTGAACCTGCTCTTCCTAGAACTGAGgttatcattg ... ttggttttagATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAA
EST: gi|47828877|gb|CK118561.1|CK118561
EST:     CTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTTCCTAGAACTGAG                         ATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCG
genomic: CTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTTCCTAGAACTGAGgttatcattg ... ttggttttagATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCG
EST: gi|86074539|gb|DR370296.1|DR370296
EST:     CTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTTCCTAGAACTGAG                         ATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCG
genomic: CTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTTCCTAGAACTGAGgttatcattg ... ttggttttagATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCG
EST: gi|47830960|gb|CK120644.1|CK120644
EST:     CTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTTCCTAGAACTGAG                         ATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCG
genomic: CTCCAGAACTTGAAGTAGTTGTTGGTGAACCTGCTCTTCCTAGAACTGAGgttatcattg ... ttggttttagATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataagcaattgtggttgttatttatgtgttgctgtgtttggcttttggttttagATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCGAGTAACAAGCGGAAGATCATCTGTGATGATGCGTTGCGTGTGGTTTTTG
                                          ctttt  CT-rich tract
               ttgttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatcattgtctttcatttatgattataatgtgtataagcaattgtggttgttatttatgtgttgctgtgtttggcttttggttttagATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCGAGTAACAAGCGGAAGATCATCTGTGATGATGCGTTGCGTGTGGTTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA