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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctattgtatgtataaacataatttggcttctgtttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC

Basic information

species Arabidopsis thaliana
transcript AT1G08860.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA19G42790.1 (Glycine max), 3'ss of exon 11
----------------ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctattgtatgtataaacataatttggcttctgtttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC
                ||   | | ||   ||  |   || || |||||  ||| |  | ||     |   ||  ||    ||| |   | |||         | ||| | |  ||||||| ||||| || ||||| || || ||||||||||||||||||| || ||||||||| ||||| ||||||||||  | | | | |||| | || ||||
gtaagcttgatatctacttcttgtgaatgaatgatt--atgaacttttcaatcattaacatgtgaagcgcaatagatccattgttttgcc-taaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGCTTTGGAGGAAAGATACCTGGTGGTACCGTATCCC

upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA03G40210.1 (Glycine max), 3'ss of exon 11
---ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctattgtatgtataaacataatttggcttctgtttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC
        | | |   |||  | | | | | |     |||| |  || | |  | ||| |||  |  ||   |   | |||         | ||| | |  ||||||| ||||| || ||||| || || ||||||||||||||||||| || ||||||||| ||||| ||||||||||  | | | | |||| |||| ||||
atgtatccttttacttcattatgttactgactaaa--ttcaataacggggtggcattg-tctgatccattgttttgcctaaccaacacagtatttatctgtagGCTATAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGATTTGGAGGAAAGATACCTGGTGGTACTGTATCCC

upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA03G40220.1 (Glycine max), 3'ss of exon 11
-----------------------------------------------------------------ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctattgtatgtataaacataatttggcttctgtttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC
                                                                       | | ||  |    || | ||| ||   |    | |  |  |||  || |||| ||||| | |     | |||||       | ||| |||  ||||| | ||||| || ||||| || || ||||||||||||||||||| || ||||||||| ||||| |||||||| |    | | | |||| |||| ||||
gtaaccttgatatctactacttgtcaatgaatgatatatgattctgagcttttcaatcattaacttatgaaacacaataaggtcctgactaacttcaatagtgggggtggcattatct-gatccattgtttttg----cctaattaacacaatatttatttgtagGCTGTAATGGAGGTTGGAGAAGTTATTCAGTTTTATGATTCTGATAGGCAGTTTCCTGCTTGGGGTTTTGGAGGGAAGCTACCTGGTGGTACTGTATCCC

upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv14s0030g00570.t01 (Vitis vinifera), 3'ss of exon 12
ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctattgtatgtata----aacataatttggcttctgt-ttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC
      |  |||    | | |   ||  ||   | | ||       | |   |  ||||  |  |||||      || |||||||     |||  ||  || |||||||| ||||| || ||||||||||| || |||||||||||||||| ||| |||||||| ||||| ||||| ||||| |||   |||||| | || || |
----acactaaatt-ccatgtttatagcttgaatgttagctcacaaaataaatcaatcttattcatgtagtgggtaatataatttcttgactgaattcctttcagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCGTATCAC

upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv12s0121g00080.t01 (Vitis vinifera), 3'ss of exon 11
ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctattgtatgtataaacataatttggcttctgt-ttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC
| |   ||   |   |  |  | | ||| ||   |                ||| ||  ||    ||  |||  |||||||      ||  ||  || |||||||| ||||| || ||||||||||| || |||||||||||||||| ||| |||||||| ||||| ||||| ||||| |||   |||||| | || || |
cactaaattccatgtttatagcttgaatgttagctcacaaaataaatcaatctttattgatgtagtgggtaa-tataatttcttgattgaattcctttcagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCGTATCAC

upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv14s0030g00550.t01 (Vitis vinifera), 3'ss of exon 8
ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctat-----tgtatgtataaacataatttggcttctgt-ttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC
       | | |   |  |   | ||  ||   | | ||       | |   |  |||| |     ||||      || |||||||     |||  ||  || |||||||| ||||| || ||||||||||| || |||||||||||||||| ||| |||||||| ||||| ||||| ||||| |||   |||||| | || || |
------gtgagaggcttatgctaatagcttgaatgttagctcacaaaataaatcaatctttattgatgtagtgggtaatataatttcttgactgaattcctttcagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAAATGATGGTACCGTATCAC

upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv14s0030g00540.t01 (Vitis vinifera), 3'ss of exon 9
ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctattgtatgtataaacataatttggcttctgt-ttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC
| |   ||   |   |  |  | | ||| ||   |                ||| ||  ||    ||  |||  |||||||     |||  ||  || |||||||| ||||| || |||||||| || || |||||||||||||||||||| |||||||| ||||| ||||| ||||| |||   |||||| |  | || |
cactaaattccatgtttatagcttgaatgttagctcacaaaataaatcaatctttattgatgtagtgggtaa-tataatttcttgactgaattcctttcagGCTATAATGGAGGTTGGAGAGGTAATACAATTTTATGATTCTGATAAGCGCTTTCCTGCATGGGGATTTGGGGGAAGGACAATTGATGGTACCATATCAC

upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv14s0030g00600.t01 (Vitis vinifera), 3'ss of exon 9
ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctattgtatgtataaacataatttggcttctgt-ttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC
| |   ||   |   |  |  | | ||| ||   |                ||| ||  ||    ||  |||  |||||||      ||  ||  || |||||||| ||||| || ||||||||||| || |||||||||||||||| ||| |||||||| ||||| ||||| ||||| |||   |||||| | || || |
cactaaattccatgtttatagcttgaatgttagctcacaaaataaatcagtctttattgatgtagtgggtaa-tataatttcttgattgaattcctttcagGCTATAATGGAGGTCGGAGAGGTCATACAATTTTATGATTCTGATAGGCGCTTTCCTGCGTGGGGATTTGGGGGAAGGACAATTGATGGTACCGTATCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattcccttgatctattgtatgtataaacataatttggcttctgtttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC
     ccttgat  putative branch site (score: 5)
                                      cttctgtttttttcc  putative PPT
             tattgtatgtataaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcagtataaaaccatcgtctcattaatttttctttcagtgtcgtgattcccttgatctattgtatgtataaacataatttggcttctgtttttttccagGCTATTATGGAAGTAGGAGAGGTCATCCAGTTTTATGATTCTGATAAGCGGTTTCCTGCCTGGGGGTTTGGAGGAAGAACATCGGATGGTTCTGTGTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - -aaaccat
- - - - - - - - - - - - - - - - ctttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacata