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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtacacctcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatgggtttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG

Basic information

species Arabidopsis thaliana
transcript AT2G33210.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 13
-gtaatgtacacctcttgtgaacatca--gactaataggctattaatgcattattagtt----tattactaatgtcgagattactcatatgggtt-tttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
 ||   | | || |  | | |  || |  || |     |    |  ||  || | ||      ||||| |  | |  | |  | |   ||   |  |||||||||| ||||| |||||  | || ||| |||| ||||| |||||||| || ||||| |||||||| || ||||| || ||||||||||||||||| ||||
agtggcgga-acattctattactattactgattctagtgactgtcctgagttgtgagcatgggtattatttttttttaaaaaaattggatctttcctttagATTGGTGGAGCTAGTGAAGCGGAGGTTGGTGAGAAGAAGGATAGAGTGACTGATGCACTAAATGCTACCAAAGCTGCTGTAGAGGAGGGTATTGTACCAG

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 13
----gtaatgtacacctcttgtgaacatcagactaataggctattaatg-cattattagtttat-tactaatgtcgagattactcatatgggttttt--agATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
      |||| |         || |  |   | |     ||||  | ||      | |  |||| |  | |  |  | ||   ||||     ||  |  |||| |||||||| |||||  | |||||| |||| ||||| |||||||| || |||||  | |||||||||||||| || || || ||||||||||| ||||
acacacaatg-atgttgagaatggaagttgaattgcactgctaggagtggtgccctgaagttatattttgacctgtatatgcatcatgacctttcctacagATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAG

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
------------------------------gtaatgtacacc-tcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatggg------tttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
                               |     |  || | ||   |||||     |  |    || || ||     |  || | |     || |   ||||       || |      ||  |||||||| ||||| || ||  |||||||| |||| ||||| |||||||| || ||||| || ||||| |||||||| || || || ||||||||||| ||||
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 12
------------------------------------gtaatgtacac-ctcttgtga-acatcagactaatag--gctattaa-tgca-ttattagtttattactaatgtcgagattactcatatgggtttt--tagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
                                    |||   ||||   ||||||   | |||  | |  ||    || |||  ||    | |  | |  || || || | | |  ||    |      |||  |||||||||||||| || ||  |||||||| |||| ||||| |||||||| || ||||| || ||||| |||||||| || || || ||||| ||||| ||||
gtgaggttattgacctactgtatgtatttacgaatggtagattacatgttcttgttttatatcgtaattgtaataactgttacctgtggctctctgatatttcctgattttgtgcctatgtgtgcatcctttcctagATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAG

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 13
---------gtaatgtacacctcttgtgaacatcagactaataggctattaatgcattattagtttattac--taatgtcgagattactcatatgggtttt-tagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
          |   ||  ||||    ||    | || || ||  | |  |    ||| ||   ||| | |   |||  |  | ||     |  |   ||||  ||||||||||||| |||||| | |||||| |||| ||||| |||||||| || |||||  ||||||| || || ||||| ||||||||||| || || ||||
gtttgtttatttgagtttaccttgcttgctgttaagtcttatctggtgcttcatcat-atggttttgtcatgataaaattaacatctgaaaccttacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCAG

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
-----------gtaatgtacacctcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatgggtttt-tagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
             | | |||    ||||  |  |  |   ||   |||  || || |  |  |  | |  |  |||     | ||     |  |   ||||  ||||||||||||| |||||| | |||||| |||| ||||| |||||||| || |||||  ||||||| || || ||||| ||||||||||| || || || |
gtttgtttatttgagtttaccttgcttgctattaggattttatctggcacttcatcctatggttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
gtaatgtacacct-cttgtgaacatcagactaataggctatt-------aatgcattattagtttattactaatgtcgagatt---actcata--tgggttttt--agATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
     |||  ||| ||||||    |  |  |||| |  |||        ||      | |    |  | | ||||   | |||   | | | |  ||   ||||  ||||||||||||| |||||  | |||||| |||| ||||| |||||||| || |||||  ||||||| ||||| || || ||||||||||| || || || |
-----gtatgcctacttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggttctgc-aatggaaaaattgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
-------gtaatgtacacctcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatgggtttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
       |  | |  | |   |    |  || |  |     |   ||   ||     ||     ||  | ||  |     ||     |     | |  ||||||||||||| |||||  | |||||| |||| ||||| |||||||| || |||||  ||||||| ||||| || || |||||||| || |||||  |||
gggggccgctacggccgctattgacaactatgatccctggtgaacatccctgtggggttctgcaatggcaaaattaacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------gtaatgtacacctcttgtgaac-atcagactaataggct-attaatg-----cattattagtttat-tactaatgtcgagattactcatatgggtttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
                                             | | |  |    ||   || | |    |||  ||  |  ||| |||       ||||     ||| ||  ||  | | |   | |    |   |||  |||| |||||||| |||||  | ||||||||||| ||||||||||| || || |||||||||||||| ||||| ||||| ||||| || || ||||| ||||
gtctgtatcaatttacaaatccccaacattactgtctaggcttgttgaggctctaaactcaggagctactgtactggtactcagattcatggggaatgttatctagatatatataaaaatggtggaaaattgcttccctttgcagATAGGAGGAGCTAGTGAAGCTGAAGTTAGTGAGAAGAAAGATAGGGTTACAGATGCTCTAAATGCTACTAAGGCAGCTGTAGAAGAAGGAATTGTACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaatgcattattagtttattactaatgtcgagattactcatatgggtttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
                     tactaat  putative branch site (score: 1)
                                                ttttt  putative PPT
        attattagtttattac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtacacctcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatgggtttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG