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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgcatctggttgtctatgatttagtttgtatagtaaagttgtactatgttcttaataagatgtttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG

Basic information

species Arabidopsis thaliana
transcript AT3G46440.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 2
-tctgcatctgg-ttgtctatgatttagtttgtatagtaaagttgtacta--tgttcttaataagatgtttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG
 | |  |   || || | | |||   | |   | ||||     |    ||  | ||||| ||    |||||||    |    || |||  || |        |||| || ||||| || |||||  | ||||||||||||||||||||||||||||| |||||||   |||||||||| ||||| ||||||
ttataaacagggattttgtctgaaagaatccct-tagtctgcataacttaatttttcttgatgccttgtttaa--ccaacatttctttcattcttgacc-atagTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 2
tctgcatctgg-ttgtctatgatttagttt-gtatagta-aagttgtactatgttcttaataagatgtttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG
| |  |   || || | | |||   | |   |||   |  |     ||   | ||||  ||    |||||||    |    || |||  || |        |||| || ||||| ||||||||  | ||||||||||||||||||||||||||||| || ||||   |||||||||| ||||| ||||||
tataaacagggattttgtctgaaagaatcccgtagtctgcataacataactttttctggatgccttgtttaa--ccaacatttctttcattcttgacc-atagTCTAACATGAGAATTTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTCGATAGATTGATGGAAAATGAAAAAAATGAG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 2
--tctgcatctggttgtctatgatttagtttgtatagtaaagttgtactatgttcttaataagatgtttaaagtgagtgc-ttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG
    |||   ||   |   |||  ||  |||  || || |  || | |  | | |||      ||  |     | | |   ||  |||  | ||      ||||| |||||||| ||| || |  | |||||||||||||| ||||| |||||||| ||||| ||  |||||||||| ||||| ||||||
acaatgctcttgtcagg--atgtcttcctttacatggtcattttttccctt-tccttgtgtgaattctcggttttactatgttcctttcatctctgacaacagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 2
-tctgcatctggttgtctatgatttagtttgtatagtaaagttgtactatgttcttaataagatgtttaaagtgagtgc-ttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG
   |||   ||   |   |||  ||| |||  ||  | |  || | |  | | ||||     ||  ||    | |     ||  |||  | ||       |||| |||||||| ||| || |  | |||||||||||||| ||||| |||||||| ||||| ||  |||||||||| ||||| ||||||
caatgctcttgtcagg--atgtcttactttacatgatcatttttttccctttccttacgtgaattcttggttttacaatgttcctttcatctctgacaaaagTCCAATATGAGAATTCTGGTTACTGGAGGAGCTGGATTTATTGGCTCTCACCTAGTTGACAAATTGATGGAAAATGAAAAAAATGAG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 3
--tctgcatctggttgtctatgatttagtttgtatagtaaagttgtactatgttcttaataagatgtttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG
  | || || ||| | |    ||   |  |  | |     ||     || | |||||     ||||  |    |    |  || |||  ||     |   |||| || ||||| || ||| |  | |||||||||||||||||||| |||||| | ||||| |   |||||||||| ||||| ||||||
tttgtgaatgtggcttttgcagaagcaactattttgcatgagcct--cttttttcttgtcttgatgccttgtttaccagtattctttcattcttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 3
--tctgcatctggttgtctatgatttagtttgtatagtaaagttgtactatgttcttaataagatgtttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG
    || || | | | |    ||   |  |  | | | | |    |  | |  |  || | |    ||       |||  || |||  || |   |   ||||| || ||||| || ||| |  | |||||||||||||||||||| |||||| | ||||| |   |||||||||| ||||| ||||||
caattgaatattgcttttgcagaagcaact-attttgcataagcctctttttcttgtattgatgccttgtttaccagtatttctttcattcttgata-acagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
-----tctgcatctggttgtctatgatttagtttgtatagtaaagttgtactatgttcttaataagatgtttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG
     ||  ||  |   || | |    | | |     |||   | |  |  |||  |||| |    ||   || ||| | | ||||   | ||      | |||||| |||||||| || ||| || | ||||||||||||||||||||||| ||  | || || |||||||||||||| ||||||||||||
tccaatcatcacattcatgccaacacatcattgcac-tagatcattacttttattatctttaactaattcctacagtaattcctttcactcttg----atggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------------tctgcatctggttgtctatgatttagtttgtatagta-aagttgtactatgttcttaataagatgt-ttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG
                                                                                        |||    |  |       | ||||  |  | |  || ||||||| |   ||  | | | ||   | || |  | | |  ||    | ||||    || ||| | || |||||||| |||||| ||||||||||||||||||| || |||||| | || || | ||| |||||| | |  |  || || 
gtaagcacgcaaatcaattcttggccagacctaattggtggaagttatgtagtccaggtttaaaacggtggttgtgattcatcgtaaactgttattactacctccagctttaactgcttttttagaagttgtgcatcgtcgtgactcagtcttgttgatttaaatatttgaggtatttttccgtttcagGCGAAGATGAGGATCTTGATCACAGGAGGAGCTGGATTCATCGGGTCTCACTTGGTCGACAGGCTCATGGAAGAGGGCACAAACGAA

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|124979880|gb|EL052874.1|EL052874
EST:     CCTCCTTCACCGTCTCCTCTCCGTAATTCCAAGTTTTGTCAG                         TCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCAC
genomic: CCTCCTTCACCGTCTCCTCTCCGTAATTCCAAGTTTTGTCAGgtaaagttat ... cattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCAC
EST: gi|116473065|gb|EG515657.1|EG515657
EST:     CAAAGCCTCCTCCTTCACCGTCTCCTCTCCGTAATTCCAAGTTTTGTCAG                         TCAAATATGAGGGTTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCAC
genomic: CAAAGCCTCCTCCTTCACCGTCTCCTCTCCGTAATTCCAAGTTTTGTCAGgtaaagttat ... cattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCAC
EST: gi|19876171|gb|AU237002.1|AU237002
EST:     CAAAGCCTCCTCCTTCACCGTCTCCTCTCCGTAATTCCAAGTTTTGTCAG                         TCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCAC
genomic: CAAAGCCTCCTCCTTCACCGTCTCCTCTCCGTAATTCCAAGTTTTGTCAGgtaaagttat ... cattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgttcttaataagatgtttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG
      tcttaat  putative branch site (score: 3)
                              tgcttttttttttttc  putative PPT
                              tgcttttttttttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgcatctggttgtctatgatttagtttgtatagtaaagttgtactatgttcttaataagatgtttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA