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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacatgcactcttgtttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG

Basic information

species Arabidopsis thaliana
transcript AT1G55810.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 5
-------ttacatgcactcttgtttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
       ||| || ||||  |  | ||  | |    |   |  | ||       | | | |   | ||| ||   |  | |      | ||| |||  |  |  ||||| |||||||| || || || ||| |||||||||| ||  ||||||||||  | || || || || ||||||||||||||||||||||| ||  |||
aagaaaattagat-cactgcttatagtttgttcttcactttatttattcatatttgttttact-ttatgttt---cagagaccctaatattt-tgac-tgctgtcagGTCAATCCTTCAGATGTAATTATTTTGGAAGGTATTCTGGTTTTCCATGATTCACGTGTCCGGGACTTGATGAACATGAAGATATTTGTTGATACAG

upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 5
-ttacatgcactct---tgtttgtc-agatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
 | | || || | |   || | ||| | || |||||  || |  |  ||  | |  |     |||| || ||   | | | | |    ||||    | ||| |||||||| ||||| || ||||||||| ||||||| || ||  ||||||||||||| || || || || |||||||| |||||||||||||| ||| |||
ataaaatacattttacatgatagtccaaatgcataatttt-tagtttta--caaagttgttgtcattctcatttcattttgtgttgccttat--cgtgttttcagGTGAACCCTTCAGATGTTATAATTTTGGAAGGCATCCTTGTTTTCCATGACCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAG

upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 5
ttacatgcactcttg-tttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG-
   |||  | || || | |  || || ||||   | |      |     |  |     |||| || ||   | | | | |   |||||   || ||| |||||||| ||||| || ||||||||| | ||||| || ||  |||||||||| || || || || || |||||||| |||||||||||||| ||| ||| 
aagcatagaatcatgatattccaaatgcatattttagcttagttttatgaagttgctgtcattctcatttcattttgtgttgctttat--catgttttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG

upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 5
ttacatgcactcttgtttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttc---tctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
  |  |    |||||  | | |  | ||| |   ||  |   ||      |||  | |   ||| |||||    |||    |  |||||   | | ||||||||| || ||  | || ||||| ||| |||||||||| ||  |||| ||||| || || |||||||  |||||||| |||||||||||||| ||| |||
-catgtttcttcttgcgttttatctccattagagtggaaatttatatggaatacaatttcagct-atacttcccttttatgttggtttaatctgt-tttgcagGTAAACCCAGCGGATGTTATTATTTTGGAAGGTATCCTTGTTTTTCATGATCCACGAGTGCGAGCATTGATGAATATGAAGATATTTGTTGACACAG

upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 5
ttacatgcactcttgtttgtcagatacataaacttgtcat-catagcctatataagaatcatgcttatactaatatttctctgt-ttatgatatatttg-cagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
      |   || ||  |          || | ||    | | |    | | |        | | |  | | | |   |||  |  ||||| ||||||| ||||| || ||||| || || |||||| ||||||| ||||||||||| ||||| | ||| || || || ||||||||||||||||||||||| ||  |||
---agggtggtcctgaatcctgtgagattatatttcaggtacttgatttctgttcccgggttacatgcattgagaaccctcattgctatgaaatatttggcagGTCAACCCTTCAGATGTGATAATTTTGGAAGGCATACTCATTTTTCATGATCTTCGTGTCCGGGAATTGATGAACATGAAGATATTTGTTGATACAG

upper sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ31180 (Selaginella moellendorffii), 3'ss of exon 4
ttacatgcactcttgtttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgc--agGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
                                                 | |  | ||| |  | || |    |              ||   |||||  |||||||| |  | || |||||||| |||||||| || ||  |||||||||||  ||| || || ||| |||||||||||||||| ||||| ||| |||
------------------------------------------------gtctgtgcatctt-ttcatccatgcacagtctgaagagccatggttttgcctagGTGAATGCAGCAGATGTTATAATCCTGGAAGGAATCCTGGTTTTCCATGACAGTCGCGTTCGTGATCTGATGAACATGAAGATTTTTGTCGACACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
                     tactaat  putative branch site (score: 1)
                        taatatttctctgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacatgcactcttgtttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA