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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtccttttcttattctctccctctcttggttgttcttcttcttcccaattgttcatacttccctaaccattttttttcttgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA

Basic information

species Arabidopsis thaliana
transcript AT1G47550.2
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os03g42750.2 (Oryza sativa), 3'ss of exon 20
----------------------------------gtaggtccttttcttattc--tctccctctcttggttgttcttcttcttcccaatt---gttcatac---ttccctaaccattttttttct------tgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA
                                   |   || ||||   ||    |||   |   |||  ||||   |  ||   || ||   |   ||||   |  |  ||| ||| | | |||      ||||| || |||||| |||||||||||||||| ||| | || || || || ||  |||| |||||| |||||||||||||||| || || || || ||     | 
gttatgtttctttcttgtgttgttcattaatcttctcaatcttttttgcatgaggtcttttttgtttgtatgtttggcacctcatcattttgtggatatacaggtgactaaactattatgtgtctgttggatgcagTCTTTATGACTTGGCTAATGTTGTGCCAACTCTTGCAAAATTCTACCATGAGGCCAGTGAATCATATGAACAAGCTTGCACTCGTCATATCAGTTCACTT

upper sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 20
---------gtaggtccttttcttattctctccctctcttggttgttcttcttcttcccaattgttcatacttccctaac-catttttttt--cttgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA
           |  ||        |   | | |    |||    |  | |  |   |   | |  ||| | |  | |    ||| || | |    ||||| ||||| ||  | || |||||||| || ||  | || |||| ||||||||| || |||||||| ||||||||||||||  | |||||||| |   |  | 
ggccgaaaaaaaactctacccaacagaatttgctatacttacgaggacctagtggcctgtactactcacattaacttggtacatgttgtatgatatgcagTCTGTACGATTTAGCAAATGTTGTACCAACACTTGCTAAGTATTATCACCAAGCTAGTGAAGCTTATGAACAAGCTTGCTCACGCCACATCAATTTAGTC

upper sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 20
---------------------------------gtaggtccttttcttattctctccctctctt--ggttgttcttcttcttcccaattgttcatacttccctaaccattt--tttttcttgc--agCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA
                                  | |   || ||   |||||  |  | | ||  |||  |||||  |   |  |       ||  ||| || |  ||||  || || ||||  ||  |||||||||| || ||||| || || ||||| || ||||||||||| ||||| |||||||| || || |||||||| || ||||| |||||  |||| 
gtaatgtttacgcatcaccctgccaaatggaggctcgaggctgtttcaattcttccattttttttaggtaattctttatacacagacaaagatatttttcacttattattttgttctttttgctcagTTTGTATGACCTTGCAAATGTCGTTCCCACTTTGGCGAAGTTTTATCATCAGGCTAGTGAAGCCTACGAGCAAGCTTGCACACGCCATATTAGTGTGATT

upper sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 20
---gtaggtccttttcttattctctccctctcttggttg-ttcttctt----cttcccaattgttcatacttccctaaccattttttttcttgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA
    | | |  |||  || ||   |   |||||  || | ||||||||     |||  |||| |    |      | || |     |||| |||||  |||||||||| || |||||||| || ||||||||||| || ||||||||||| |||||| | |||||||||||||| | ||| || ||||||||||| 
gtatttgtttatttattttttgcatgattctctaagtagattcttcttatgatttcttaattctaaggatcctgattac-agacagtttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCAGGCCAGTGAATCTTATGAACAAGCTTGCATGCGGCATATTAGCATGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcttcttcttcccaattgttcatacttccctaaccattttttttcttgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA
                               ccctaac  putative branch site (score: 2)
                            cttccctaaccatttt  CT-rich tract
                                  taaccatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtccttttcttattctctccctctcttggttgttcttcttcttcccaattgttcatacttccctaaccattttttttcttgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT