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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttaccagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA

Basic information

species Arabidopsis thaliana
transcript AT4G11030.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
----gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttacc--agGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA
      ||  ||||    |    || | | ||   ||||||   || |    |   || |||     ||||| |  | |    | | ||| |       ||||||||   ||| ||  |||||||||||||  |  |||||||||||||||| ||||| || || |||||||||||||| ||| | |||||||| ||||||||||| |||||
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgc---ttcttgt--aaccggctcactttga-------tatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA

upper sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttaccagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA
  ||||        | | ||| ||      |  |  | ||| ||||       ||  |   |       |||     | || |   | || |      ||| | ||| ||  ||||||||||||||||  ||||||| ||||| || || || || |||||||| |||||||| ||  | |||||||| ||||| || || || ||
--tactctcttttactaaactgtgcctggatgacagtacta-atatgatcagctagttgcaaagagaggtttgaa--aattgaaacatctgttctctgcttgc-agGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA

upper sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
gttactaaaaacctcaacactttgatcattttgctttcctatatata-gcattttaaatatcagttcttatttaccttatttaat-ttaactatgtgtatcttac-cagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA
           | | ||     |  | ||||  ||| ||   | | | || ||| |||| |       | |     || || | |   || |||   ||| |    |||| ||  |||||||||||||  |  | |||||||||||||| |||||||| || |||||||||||||| ||| | || |||||||| || || ||||||||
---------gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcactgccaaatattaatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA

upper sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 15
gttactaaaaacctcaacactttgatcat--tttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttaccagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA
|||| |  |    |     |    ||     |||   ||| ||||| |||| | ||   | |  ||    |||| |||| | |     ||  || | |   | | |||| ||| |||| ||||||||||| |||||||||||||| || ||||| ||||| ||||| || || || ||  | |||||||| ||||| ||||| || ||
gttatttcatttatgttttccaaaattgaggtttatattcttatat-tagc-tgttgggt-tgggtcacaattttccttttattcacaaatgatatat---tcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA

upper sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatctt-accagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA
|||| |  |    |  |   |||    ||||    ||  |||   ||   | |||  | |  | ||  | ||  | | ||||  ||||| |    ||| || | |||| ||| |||| ||||||||||| || ||||||||||| || ||||| ||||| ||||| || || || ||  | |||||||| ||||| ||||| || ||
gttatttca----tttatgttttccaaatttgaggtttatattctta---tattagctgttgggtcacagttttccttttta--ttaacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA

upper sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 15
-gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttaccagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA
  || || | |    ||   |||     |||  | |||    |        || |  ||     |  |||   |||||  | |   | |||   | | | ||  |||| ||||||||||||||||||||  |||| |||||||| || || ||||| || |||||||| ||||| ||  | |||||||| || || || ||||||||
gtttgctcatattggcatttcttcttgaattaagttttgaggtcctctattttgtggattcgtttctttaacaaccttgctga---tgact---tatcttttcacagGGGATGTTGGTGAGTGGCAACCTGATGGGAGCATGAAAATTATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAA

upper sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttaccagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA
|| || || |  |     |     |  ||   | ||   || |   |   |  |  |    ||  || || ||   |  ||  ||| |  |||  |     | |||||||| |||| ||||||||  || |||| ||||||||||| |||||||| || ||||| || ||||| ||  | || ||||| ||| | || || || ||
gtcaccaatatacgtggaaaa--aacgatgcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattc-ttttataatgcatga---atcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttaccagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA
                               atttaac  putative branch site (score: 3)
                                              tcttacc  putative PPT
            ttcttatttaccttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttaccagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT