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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctatgcttatattctctttcccctttccatatgtcttctattagccagtggttcagctaaatagtagtctttgttggagtcgttgctgttatcttaaccagttatatacagATGACCAATACGATCCAGAAGAAATATAAGGTTTCATCCACCCAACTTCTGTATCAGTCTTGCCCATATCAAGCAATCACACTTTTTGTTACTGGCCCAT

Basic information

species Arabidopsis thaliana
transcript AT2G30460.2
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 5
gtatcctatgcttatattctctttcccctttccatatgtcttctattagccagtggttcagctaaatagtagtctttgttggagtcgttgctgttatc-ttaaccagttatatacagATGACCAATACGATCCAGAAGAAATATAAGGTTTCATCCACCCAACTTCTGTATCAGTCTTGCCCATATCAAGCAATCACACTTTTTGTTACTGGCCCAT
        |  | | | |   | |    |||||   ||     ||| | |   |  | ||  ||| |    || ||| |       ||| |||| ||| || |||  | ||   |||||||| || || ||||||||||| |  ||||| ||||| |||||||| || || ||||||||||| |||||| || | || || ||| | | |||||| |
--------tagtaacacttggtgtgt--tttcctcctgctgcatat-aactcttaatgcatttaagtttctgttttttt---gtctgttcctgtaatccttgaccgttcat---cagATGACAAACACTATCCAGAAGAAGTTCAAGGTCTCATCGACCCAACTGCTCTACCAGTCTTGCCCTTATCAATCACTGACCCTGTTTCTCATTGGCCCCT

upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 5
gtatcctatgcttatattctctttcccctttccatatgtcttctattagccagtggttcagctaaatagtagtctttgttggagtcgttgctgttatcttaaccagttatatacagATGACCAATACGATCCAGAAGAAATATAAGGTTTCATCCACCCAACTTCTGTATCAGTCTTGCCCATATCAAGCAATCACACTTTTTGTTACTGGCCCAT
            |||      |     |||| || | ||   || |  ||   |       ||      |  | |||  |   | |||   |||   |||||  |||  | |  ||||||| ||||| ||||||||||| || |||||||| |||||||| ||||||||||| || || ||||||||||||   || || ||  || |||||||||
------------tattgcacttgaaagctttacaaaggtgg-ctgtctgcttttttcattcctgggctatcattttttatctgggcgtc-ttgtc--cttaattagtggtttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATTTCTGGCCCAT

upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G39920.1 (Glycine max), 3'ss of exon 5
gtatcctatgcttatattctctttcccctttccatatgtcttctattagccagtggttcagctaaatagtagtctttgttggagtcgttgctgttatcttaaccagttatatacagATGACCAATACGATCCAGAAGAAATATAAGGTTTCATCCACCCAACTTCTGTATCAGTCTTGCCCATATCAAGCAATCACACTTTTTGTTACTGGCCCAT
              ||||    ||      |  |||    |    ||  |   |  ||    |     |   || || ||    | |     ||   |||||| |||    |  ||||||| ||||| ||||||||||| || |||||||| |||||||| ||||||||||| || || ||||||||||||   || || ||  |  |||| ||||
--------------tattgcacttgaaagctttataaaggtg--gttgtctgcttttttcattcctgggctatcattttttatttgggcatcgtgtccttaactagtggcttttagATGACAAATACTATCCAGAAGAAGTACAAGGTTTCTTCCACCCAGCTTCTGTATCAATCATGTCCATATCAAGCAGCAACCCTGTTAATCGCTGGTCCAT

upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 6
gtatcctatgcttatattctctttcccctttccatatgtcttctattagccagtggttcagctaaatagtagtctttgttggagtcgttgctgttatcttaaccagttatatac--agATGACCAATACGATCCAGAAGAAATATAAGGTTTCATCCACCCAACTTCTGTATCAGTCTTGCCCATATCAAGCAATCACACTTTTTGTTACTGGCCCAT
             | |     |       | |  | |    ||  ||   |  |  ||| ||   ||||||   ||| ||   || |||  |   ||||||| ||||||||| |  ||||||||||||  ||||||||||| |  |||||||| || |||||||| ||||||||||| || || |||||||| || ||| | ||  || |||||||||
-------------acaagtagtcgtggaatgcattgtaggatcagtt--tctttctttctgcaggatagtaaaatttctttt-gttgtt--taagatcttaatcagttatattcttagATGACCAATAACATCCAGAAGAAGTTCAAGGTTTCTTCTACCCAACTCCTGTATCAGTCATGTCCTTATCAAGCCATGACATTGTTCATTGCTGGCCCAT

upper sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 6
gtatcctatgcttatattctctttcccctttccatatgtcttctattagccagtggttcagctaaatagtagtctttgttggagtcgttgctgttatcttaaccagttatatacagATGACCAATACGATCCAGAAGAAATATAAGGTTTCATCCACCCAACTTCTGTATCAGTCTTGCCCATATCAAGCAATCACACTTTTTGTTACTGGCCCAT
         |  |  |||    |    |  |   ||| || ||||   ||| ||  ||  | |   || || | |||     |||| |   |   ||||||| |||||   |  ||||||| ||||| ||||||||||| |  |||||||| || || ||||| |||||||| ||||| || ||||||||| | || || ||  |  |||||||||
--------aggctgcatttatgtgtttcaataactatttcctctag-ggcctgtctttgtgtt--gtaataatgttt-----agtcttgtttaagatcttaatcagttccttttagATGACGAATACCATCCAGAAGAAGTTCAAGGTTTCTTCAACGCAACTGCTGTATCAATCTTGTCCCTATCAAGCACTGACGCTGTTCATCTCTGGCCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaatagtagtctttgttggagtcgttgctgttatcttaaccagttatatacagATGACCAATACGATCCAGAAGAAATATAAGGTTTCATCCACCCAACTTCTGTATCAGTCTTGCCCATATCAAGCAATCACACTTTTTGTTACTGGCCCAT
 tatcttaac  putative branch site 
                                ttatcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctatgcttatattctctttcccctttccatatgtcttctattagccagtggttcagctaaatagtagtctttgttggagtcgttgctgttatcttaaccagttatatacagATGACCAATACGATCCAGAAGAAATATAAGGTTTCATCCACCCAACTTCTGTATCAGTCTTGCCCATATCAAGCAATCACACTTTTTGTTACTGGCCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA