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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggttagagtttatgagtattttttttggctttgtgattttagaaaagttgattaagacaagtttggagttgaatctaatcataaaattatttaaatagGGTTTCAGAAAGGTGAATCCGGATCGGTGGGAGTTTGCAAACGAAGGGTTTCTTAGAGGGCAAAAGCATCTCCTCAAGAACATAAGGAGAAGAAAAACAA

Basic information

species Arabidopsis thaliana
transcript AT3G22830.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G22830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os07g08140.1 (Oryza sativa), 3'ss of exon 1
--------atggttagagtttatgagtattttttttggctttgtgattttagaaaagttgattaagacaagtttggagttgaatctaatcataaaattatttaaatagGGTTTCAGAAAGGTGAATCCGGATCGGTGGGAGTTTGCAAACGAAGGGTTTCTTAGAGGGCAAAAGCATCTCCTCAAGAACATAAGGAGAAGAAAAACAA
         |    |||    |  || ||  | ||  || |  |  | | |||   ||   ||   || |   |     ||||   |||  |    || |||    ||||||||||||||||| |||| ||||||||||| |||||||| ||    |||||  | || || |  ||||| ||||||||||| | | | |||||| || 
ttctccccctaccaagaaagaagtagcatcctgtt--gcatacttgtctaagat--gtctcttgcaactaacatttccctgaag--aattgtttgtttgtttt--cagGGTTTCAGAAAGGTGGATCCTGATCGGTGGGAATTTGCAAATGAGAATTTTCTGCGGGGACAGAGACATCTTCTCAAGAACATCAAGCGTAGAAAACCAC

upper sequence: AT3G22830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os10g28340.3 (Oryza sativa), 3'ss of exon 2
----------------------atggttagagtttatgagtattttttttggctttgtgattttagaaaagttgattaagacaagtttggagttgaatctaatcataaaattatttaaatagGGTTTCAGAAAGGTGAATCCGGATCGGTGGGAGTTTGCAAACGAAGGGTTTCTTAGAGGGCAAAAGCATCTCCTCAAGAACATAAGGAGAAGAAAAACAA
                      |  ||   |  |   ||| | || |  |    || | |  || | |        |      |   ||| | ||  | |  |||| ||| | |    | |||| |||||||||||  |||| ||| |||||||||||||||| || || ||||| || || |||| ||||||||| || |  |||| |||||| ||  |  
gtcattctttcactaaaaagctacagtctaaaatctagagcagttatcctaatctt-tcacgttggcatgtgcatctggccttacaatggtgatgtttgtc-tcattaaaatct----acagGGCTTCAGAAAGGTCGATCCTGATAGGTGGGAGTTTGCAAATGAGGGTTTTCTCAGGGGCCAAAGGCATCTCCTGAAAACGATAAAGAGAAGGAAGCCCC

upper sequence: AT3G22830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os10g28340.5 (Oryza sativa), 3'ss of exon 1
------atggttagagtttatgagtattttttttggctttgtgattttagaaaagttgattaagacaagtttggagttgaatctaatcataaaattatttaaatagGGTTTCAGAAAGGTGAATCCGGATCGGTGGGAGTTTGCAAACGAAGGGTTTCTTAGAGGGCAAAAGCATCTCCTCAAGAACATAAGGAGAAGAAAAACAA
      |  ||   |  |   ||| | || |  |    || | |  || | |        |      |   ||| | ||  | |  |||| ||| | |    | |||| |||||||||||  |||| ||| |||||||||||||||| || || ||||| || || |||| ||||||||| || |  |||| |||||| ||  |  
aaagctacagtctaaaatctagagcagttatcctaatctt-tcacgttggcatgtgcatctggccttacaatggtgatgtttgtc-tcattaaaatct----acagGGCTTCAGAAAGGTCGATCCTGATAGGTGGGAGTTTGCAAATGAGGGTTTTCTCAGGGGCCAAAGGCATCTCCTGAAAACGATAAAGAGAAGGAAGCCCC

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|116420134|gb|EG462726.1|EG462726
EST:     TCTTCAAGCACAATAACTTCTCCAGTTTTGTCCGCCAGCTCAACACATAT                         GGTTTCAGAAAGGTGAATCCGGATCGGTGGGAGTTTGCAAACGAAGGGTTT
genomic: TCTTCAAGCACAATAACTTCTCCAGTTTTGTCCGCCAGCTCAACACATATgtaagtccta ... atttaaatagGGTTTCAGAAAGGTGAATCCGGATCGGTGGGAGTTTGCAAACGAAGGGTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagttgattaagacaagtttggagttgaatctaatcataaaattatttaaatagGGTTTCAGAAAGGTGAATCCGGATCGGTGGGAGTTTGCAAACGAAGGGTTTCTTAGAGGGCAAAAGCATCTCCTCAAGAACATAAGGAGAAGAAAAACAA
                             atctaat  putative branch site (score: 3)
                       agttgaatctaatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggttagagtttatgagtattttttttggctttgtgattttagaaaagttgattaagacaagtttggagttgaatctaatcataaaattatttaaatagGGTTTCAGAAAGGTGAATCCGGATCGGTGGGAGTTTGCAAACGAAGGGTTTCTTAGAGGGCAAAAGCATCTCCTCAAGAACATAAGGAGAAGAAAAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - -tttttgg
- - - - - - - - - - - - - - - - - - - - - agaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aagacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cataaaa