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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtagaactctttgcttttgtcccgcggaaggaactgcaaacatgtatgttgattgttgtgtctatttgtttcctgtatagtactttgttattcacttgttccttttgcagTTGTTTTTATTGGATCAACCCTGTTTGCTTTGCAACAGCTATCTGGTATAAATGCTGTTTTTTATTTCTCTTCTACCGTATTCAAAAGTGCTGGAGTACC

Basic information

species Arabidopsis thaliana
transcript AT1G67300.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G67300.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 9
gtatgtagaactctttgcttttgtcccgcggaaggaactgcaaacatgtatgttgattgttgtgtctatttgtttcctgtatagtactttgttattcacttgttcctttt----gcagTTGTTTTTATTGGATCAACCCTGTTTGCTTTGCAACAGCTATCTGGTATAAATGCTGTTTTTTATTTCTCTTCTACCGTATTCAAAAGTGCTGGAGTACC
    ||| ||    ||   | | | ||           ||     || |  | | |    |     ||||| | |   |  | | | ||||||  | ||  || ||||||     ||||||||||||||||  |||| || |||||||| |||||| |||| || |||||| |||| || |||||||| || || || |||| |||||  || || ||
----gtacaagctgttatgtgttttccattctg----ttgtg--tatttgcgctaaactataaccttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC

upper sequence: AT1G67300.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G412899_T05 (Zea mays), 3'ss of exon 9
gtatgtagaactctttgc---ttttgtcccgcggaaggaactgcaaacatgtatgttgattgttgtgtctatttgtttcctgtatagtactttgttattcacttgttccttttgcagTTGTTTTTATTGGATCAACCCTGTTTGCTTTGCAACAGCTATCTGGTATAAATGCTGTTTTTTATTTCTCTTCTACCGTATTCAAAAGTGCTGGAGTACC
|||        ||| |     ||||||   |   | |||  |  ||  |  |  ||| |       |||| | |||    | |   || | ||   | |  ||| ||  |  | ||||||||||||||||  |||| || |||||||| |||||| |||| || |||||| |||| || |||||||| || || ||||||| |||||  || || ||
gtacaagctgttctatatcctttttgttgtgtttatggacttctaataacctgagttca-------gtctgtctgtgaagttt---gttcattacaagttccttttt--tggtacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCC

upper sequence: AT1G67300.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G09270.3 (Glycine max), 3'ss of exon 9
gtatgtagaactctttgcttttgtcccgcgga---aggaactgcaaacatgtatgttg--attgttg--tgtctatttgtttcct---gtat-----agtactttgttattcacttgttccttttgcagTTGTTTTTATTGGATCAACCCTGTTTGCTTTGCAACAGCTATCTGGTATAAATGCTGTTTTTTATTTCTCTTCTACCGTATTCAAAAGTGCTGGAGTACC
||||| |    || | | || | ||  |   |     ||  ||  |   | | ||      |||||   ||   | | |||||||   || |     |||  ||| ||||||||  |||| |||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||| |||||||||||||| || || || |||||||||||||| ||
gtatgcatttttcctggtttgtctctgggatagttgtgacttgtgagtgtatttgccattgttgttatctggtcactggtttccttaggtttccaaaagttattttttattcacaagttcgttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAATGCTGTGTTTTATTTCTCTTCAACTGTTTTTAAAAGTGCTGGAGTGCC

upper sequence: AT1G67300.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G32510.1 (Glycine max), 3'ss of exon 9
gtatgtagaactctttgcttttgtcccgcggaaggaactgcaaacatgtatgttgattgttgtgtctatttgtttcctgtatagtactttgttattcacttgttccttttgcagTTGTTTTTATTGGATCAACCCTGTTTGCTTTGCAACAGCTATCTGGTATAAATGCTGTTTTTTATTTCTCTTCTACCGTATTCAAAAGTGCTGGAGTACC--------------------------------------------
                                                                                                                       ||||||||||||||||| |||||||| |||||||||||||||||||||||||| |||||||||||||| || || || |||||||||||||| ||                                            
-----------------------------------------------------------------------------------------------------------------------tttattggatcaaccctatttgctttacaacagctatctggtataaatgctgtgttttatttctcttcaactgtttttaaaagtgctggagtcccatcagACATTGCAAATGTCTGCATAGGAATCGCTAATTTGGCAG

upper sequence: AT1G67300.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv11s0016g03660.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------gtatgtagaactctttgcttttgtcccgcgga--aggaactgcaaacatgtatgttgattgttgtgtctatttgtttcctgtat-----agtactttgttattcacttgttccttttgcagTTGTTTTTATTGGATCAACCCTGTTTGCTTTGCAACAGCTATCTGGTATAAATGCTGTTTTTTATTTCTCTTCTACCGTATTCAAAAGTGCTGGAGTACC
                                  || |||     | ||  | | ||    | |    |   | |||         ||  |    || |   ||||    |  ||  |     | | |||||| |||||||  |||||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||| |||||||||||||||||||| || ||||| ||||| || ||||| ||
gtagatatgatacttctttggtatgcacctatgagtttgtgagtatgttctcgtctgctttgagatttactgagtgctgctgctgttgccggcacttcttcttattctccttttgcctccaagaatgctttgt-attcactgattccttttgcagTTGTTTTTATTGGATCAACCCTATTTGCTTTACAACAGCTATCTGGTATAAACGCTGTTTTTTATTTCTCTTCCACTGTATTTAAAAGCGCGGGAGTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtctatttgtttcctgtatagtactttgttattcacttgttccttttgcagTTGTTTTTATTGGATCAACCCTGTTTGCTTTGCAACAGCTATCTGGTATAAATGCTGTTTTTTATTTCTCTTCTACCGTATTCAAAAGTGCTGGAGTACC
                                   ttcacttgttcctttt  CT-rich tract
       tatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtagaactctttgcttttgtcccgcggaaggaactgcaaacatgtatgttgattgttgtgtctatttgtttcctgtatagtactttgttattcacttgttccttttgcagTTGTTTTTATTGGATCAACCCTGTTTGCTTTGCAACAGCTATCTGGTATAAATGCTGTTTTTTATTTCTCTTCTACCGTATTCAAAAGTGCTGGAGTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA