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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT

Basic information

species Arabidopsis thaliana
transcript AT1G01320.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 16
--------gtctgtatatattatatgg----ttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattt----tgttaaaa---cagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
        || |  ||  |||| |       | ||| ||||||   ||    || |   | |      ||   || |   ||    |   ||||   |||||||| || ||||||||||||||  ||||||||||||||||||||||||| || ||||| || |||||||||||||||||||| ||||||||||| ||||
caacatgagtattgattaattaaagaagaattgagaatgtgatgaattgaagttttgaaaaataccccaagtcaatatgcttatcatagaaaaaatgcagGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT

upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 18
------------gtctgtat-atattatatggttagattgtgatatctttcctttatatgac--aattgtgaaactaaaagattttg--ttaaa--acagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
            || | |   | | ||| |  |    || |||| |  |    ||  | ||    |||   |  |   ||| ||||   |||||   ||||||||||| ||||| ||||| ||||| || ||||| ||||| ||  | || || |||||||| ||||| |||||||| ||||| ||||||||||| ||||
atttcagccattgtttatgccaaaatatctattctctttttgatttagtagagtttcaggatttgatttcaattcatcaagttttttacttaaatcgcagGCTACAATTTATCAACAAAAAGCTTTGGATATCAACGAGAGAGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT

upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 18
------------------gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaa--acagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
                  | |   |||| || | |  ||    | |  ||   || ||  || |||      |  | | ||    |||  |||||   |||||||| || ||||| ||||| ||||| || ||||| ||||||||  | || || |||||||| ||||| |||||||| ||||| ||||||||||| ||||
ttgtttatttgcacctatgccaaaatatcttttctcttttagatttagtaaagtttctggatttgatttcaattcatc-aagttttttacttaaatcgcagGCTACCATTTATCAACAAAAAGCTTTGGATATCAACGAGAGGGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT

upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtct-gtatatattatatggttagattgtgatatctttcctttata-----tgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
              ||| |  | |   |  |   |  ||  || | | |||  ||| ||     || | ||| | ||   || || | |    |    |||| ||||| ||||| |||||||| || |||||||||||||| ||||| ||||||||||||||||| || |||||||||||||| ||||||||||| ||||
tatggtttttcccatctagggttttccacgtaaatctatgctgtttttttttttttttacttgttgcctattcttaattcaagagttgtcccaattcaagGCCACAATTTATCAACAAAAGGCATTGGACATCAATGAGAGAGAACTAGGACTTGATCATCCAGACACGATGAAGAGTTATGGAGATCTTGCTGTGTTCT

upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 18
--------------gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaa---aagattttgttaaaa--cagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
                |||| | | || | |  ||   ||||    | ||  | || |   | || | |     |||   |||| ||     ||   ||||| ||||| ||||| |||||||| || |||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||| ||||||||||| ||||
tccatgtaaatctatgctgtttttttttttttttttccttgttgcctattctcatttttccataactatatggttaattcaagagttgtcccaatttcagGCCACAATTTATCAACAAAAGGCGTTGGACATCAATGAGAGAGAACTAGGACTTGATCATCCAGACACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT

upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
                |    | |  |  | || ||   || || | |    ||    | |  | || ||| |   | ||||| |  ||||| |||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| ||||||||||| || ||||||||  | |||||||| |
---------------gtacacaaaa-gctacatattgtattaatgtaattgatgacttaattgatgactttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT

upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: EFJ26734 (Selaginella moellendorffii), 3'ss of exon 17
gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
                  ||  | |  ||  | ||| |  || ||| |||||    |   |    ||   |  |    |||||||| || || || |||||||||||||||||||||||  | || |||||  | || ||||| ||||| |||||||| ||||| ||||| |||||||| |
------------------gtctggtcttgtca-cttgcggttttat-acaatctaaacgtttgtcgacgcttct----cagGCTACCATCTACCAACAAAAGGCTTTAGACATCAATGAACGCGAGCTTGGCTTGGACCATCCGGATACCATGAAGAGCTATGGAGATCTGGCTGTCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
                               aactaaa  putative branch site (score: 2)
                                         ttttgtt  putative PPT
                              aaactaaaagattttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT

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