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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttggacaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC

Basic information

species Arabidopsis thaliana
transcript AT2G47470.4
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 7
gtaagttggacaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaag--taccttata---ttcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC
 |    ||| || || ||  |  | |    | |    | ||       ||||   |||||| |  | |  ||||||         | | ||||    || |||||||||||   ||| |  || |||||||| |||||||||||||  |||||||||||| | ||||| || || |||||||| || ||||||||||| |  
atgttatgggcatgc-ttccagcactttaaactcatgtcttgttctatattttgatttcatgatgc-actacataagttttgacttgctttatgacttttagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
-----gtaagttggacaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC
      |||  |  |||  | | || |||       | |   || | |      ||| | || |  | ||  | ||  |  |  || | |    |  ||||| ||||||||   ||| ||||| ||||||||||||||||||||||  |||||||||||| | |||||||| || ||  | || || |||||||| || |  
tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccataag-agaatttttaatcatgcatgccac-ttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: AC217311.3_FGT007 (Zea mays), 3'ss of exon 1
gtaagttggacaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC
                                      || |  | || |  ||||| || |  | |   | ||||  | |  |||||    | ||||||||| ||   ||| ||||| |||||||| |||||||| ||||  |||||||| ||| | |||||||| |||||| |||| || ||||||||||| |  
--------------------------------------gtatgcattcttccatgtt-cacagcatcttta-ataataata--tacctc---tgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G159369_T01 (Zea mays), 3'ss of exon 7
-gtaagttggacaggcattttatta---ataccgattt-tactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC
 |  ||   |  ||| ||   |  |   ||  | |||| || |   ||   |  |   |  |||  |    || | |||    |  | ||     | | ||||||||| ||   ||| ||||| |||||||| |||||||| ||||  |||||||| ||| | |||||||| |||||| |||| || ||||||||||| |  
tgacagactgttagggataacacaacctatgacaatttataataactacgtttgtcctttcttc-catgttcacagcatctttaataatatacc-tctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G008647_T02 (Zea mays), 3'ss of exon 4
-gtaagttggacaggcattttattaataccgattt-tactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaagtacctta--tattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC
   |||          | | ||   ||  | |||| || |   ||   |  |   |  |||  |    || | |||    |  | ||   ||  | | ||||||||| ||   | | ||||| |||||||| |||||||| ||||  |||||||| ||| | |||||||| |||||| |||| || ||||||||||| |  
caaaagcatctttaataatatacctatgacaatttataataactatgtttgtcctttcttc-catgttcacagcatctttaataataatatacctctgcagATATGGTGTTTCTAGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G110742_T02 (Zea mays), 3'ss of exon 7
gtaagttggacaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC
                                      || |  | || |  ||||| || || | |   | ||||  | |  |||||    | ||||||||| ||   ||| ||||| |||||||| |||||||| ||||  |||||||| ||| | |||||||| |||||| |||| || ||||||||||| |  
--------------------------------------gtatgcattcttccatgtt-cacaacatcttta-ataataata--tacctc---tgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 6
----------------------------------------------------------------------------------------------------gtaagttgg--acaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC
                                                                                                    | |   | |  ||  | ||||  ||   ||  ||   ||  | | |  ||     ||||  |||    ||| | |        |  ||  || || ||| |||||||| |||||||| || || ||||| || ||||||||||  |||||||||||| | |||||||| || |  ||||| || | ||||||||| |  
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacg--caatatactgtacttatcacactacat-cagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G404011_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------------------------------------------gtaagttggacaggcattttattaataccgattttactgtttaa-agtcatttatgtttcataaaaccaaaacataaagacaagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC
                                                                                                       || ||   |||| ||   |  | |     | |    |||| | ||  ||  ||||| || || | |   | ||||  | |  |||||    | ||||||||| ||   ||| ||||| |||||||| |||||||| ||||  |||||||  ||| | |||||||| |||||| |||| || ||||||||||| |  
gtatgcattctgacttgtctatttcagtggttgttatgcacattagctttcagcctttagtttaacaccattggattttcttatatggcgattgtgatgaaaaaatttcctcaggaatcacagaagtgattctctcgtcgtttgacagatatggatgtt-cacaacatcttta-ataataata--tacctc---tgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGTCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
gtaagttggacaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagac-----aagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC
 || | |||  | | |    |  ||| ||         | | ||  |    ||| |   | |  |  || |  | |||        | ||   | ||| ||| ||||  ||||||||||| || || ||||| ||||||||||||| ||||||||||||| | || || |  ||||| || || || |||||||||||    
ttacggtggttaagaaaacaaaaaat-ccagcgaagaggataaagatggaatat-tacaacatgataaataattgaagtttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G01820.1 (Glycine max), 3'ss of exon 8
---gtaagttggacaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC
     |   | | |   | ||  | | |||  |   |      |   | || ||      | |||||      |  |       | ||   | ||| ||| || |  ||||||||||| || || ||||| ||||||||||||| ||||||||||||| | || || |  ||||| || || || |||||||||||    
tattcatagttgtcttcctttcaagtcataatgtgatggaatatacgaatcgttacaacatgataaataattgaagtttgctggaataatatttatgcagGTACGACGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGACTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G01750.3 (Glycine max), 3'ss of exon 7
gtaagttggacaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagac-----aagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC
 || | |||  | | |    |  ||| ||         | | ||  |    ||| |   | |  |  || |  | |||        | ||   | ||| ||| ||||  ||||||||||| || || ||||| ||||||||||||| ||||||||||||| | || || |  ||||| || || || |||||||||||    
ttacggtggttaagaaaacaaaaaat-ccagcgaagaggataaagatggaatat-tacaacatgataaataattgaagtttgctggaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

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|124811516|gb|EH896382.1|EH896382
EST:     GTAGTCATCGCCAATTTGGATGCTGATGCACACAAAGCCCTTGGCGAGAA                         ATATGGAGTGAGTGGATTCCCAACA
genomic: GTAGTCATCGCCAATTTGGATGCTGATGCACACAAAGCCCTTGGCGAGAAgtaagttgga ... ttatattcagATATGGAGTGAGTGGATTCCCAACA
EST: gi|164188777|gb|ES024382.1|ES024382
EST:     TTGGATGCTGATGCACACAAAGCCCTTGGCGAGAA                         ATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAA
genomic: TTGGATGCTGATGCACACAAAGCCCTTGGCGAGAAgtaagttgga ... ttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAA
EST: gi|164130240|gb|EL999537.1|EL999537
EST:     CAAAGCCCTTGGCGAGAA                         ATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAA
genomic: CAAAGCCCTTGGCGAGAAgtaagttgga ... ttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAA
EST: gi|125218750|gb|EL232833.1|EL232833
EST:     GTAGTCATCGCCAATTTGGATGCTGATGCACACAAAGCCCTTGGCGAGAA                         ATATGGAGTGAGTGGATTCCCAA
genomic: GTAGTCATCGCCAATTTGGATGCTGATGCACACAAAGCCCTTGGCGAGAAgtaagttgga ... ttatattcagATATGGAGTGAGTGGATTCCCAA
EST: gi|124725939|gb|EH817341.1|EH817341
EST:     TCGCCAATTTGGATGCTGATGCACACAAAGCCCTTGGCGAGAA                         ATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAAGGACA
genomic: TCGCCAATTTGGATGCTGATGCACACAAAGCCCTTGGCGAGAAgtaagttgga ... ttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAA-GGACA
EST: gi|116441306|gb|EG483898.1|EG483898
EST:     GTAGTCATCGCCAATTTGGATGCTGATGCACACAAAGCCCTTGGCGAGAA                         ATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAA
genomic: GTAGTCATCGCCAATTTGGATGCTGATGCACACAAAGCCCTTGGCGAGAAgtaagttgga ... ttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAA
EST: gi|125045498|gb|EL117767.1|EL117767
EST:     GTAGTCATCGCCAATTTGGATGCTGATGCACACAAAGCCCTTGGCGAGAA                         ATATGGAGTGAGTGGATTCCCAA
genomic: GTAGTCATCGCCAATTTGGATGCTGATGCACACAAAGCCCTTGGCGAGAAgtaagttgga ... ttatattcagATATGGAGTGAGTGGATTCCCAA
EST: gi|124813865|gb|EH898731.1|EH898731
EST:     GTAGTCATCGCCAATTTGGATGCTGATGCACACAAAGCCCTTGGCGAGAA                         ATATGGAGTGAGTGGATTCCCAACATTGAAATT
genomic: GTAGTCATCGCCAATTTGGATGCTGATGCACACAAAGCCCTTGGCGAGAAgtaagttgga ... ttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtcatttatgtttcataaaaccaaaacataaagacaagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC
      atttatgtttcataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttggacaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG