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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataaaatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG

Basic information

species Arabidopsis thaliana
transcript AT5G43810.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 19
-------gtacgaaacaa-ctatcgaaatatccgttaatatgaccttttccgtaactatacag-ataaaatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
         |  ||| |  || ||   |    || |   ||    ||  ||     | | |   ||  | ||| |    |  ||| ||| |  |  || |||||||||| ||||| || || ||||| || |||||||| |||||||||||||| ||||| |  || ||  |  |||| ||||| || || || ||     
acttggatcagcaaatattctgtctgtagtagcgctggaatataattccccaagtttgtcctccatgtactgaaatgactgatgtgtgt-gagttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC-----

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
-gtacgaaacaactatcgaaatatccgt--taatatgaccttttccgtaactatacagataaaatg---acactgt-ttgtgtttgttg-tatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
  |   || ||  |      | | || |  || |  || |  |  | |    ||| ||  | | |      |||||  ||   |   ||   ||    |||||||||| ||||| || || |||||||| || ||||| |||||||||||||||||||| |  || ||| | ||||| ||||| || || || ||     
ccttttaatcatgtgattgtacagccatggtacttggatcagtagcatgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC-----

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 19
gtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataaaatg---acactgttt----gtgtttgttgtatgat----ctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
  |  |    | | |  |  | |  | || |  || |  |  | |    ||  ||  | | |      ||| |       ||  || ||| |||     | ||||||| || |||||||| || |||||||| || ||||| |||||||||||||||||||| |  || ||  |  |||| ||||| || || || ||     
--atcatgtgattgtacagct-tatggtacttggatcagtagcatgggaatgtagtcagactctccgtactatactggaatgactgatgtgtgagtttgccagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC-----

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 11
-----gtacgaaacaac-tatcgaaatatccgttaat-atgaccttttccgtaactatacagataaaatgacactgt---ttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
     ||| |    |   ||| ||  | |  |||  | |||| | | |   |  ||| ||   ||  ||   | |||   || ||||| |  ||| ||  |||| || ||  | || || ||||| |||||||| ||||| || ||||| |||||||||||||| ||||| ||| |||| ||||||||||||||||| ||||
tataagtatgtcctattatatggacttgtttgttttttatgagcatataaat--ctaaacctttatgattcaattgtggtttttgtttctattatcatgcagGGTACGAGTCGTCCAGCTCATTATCATGTTCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTTTGACAAACAATCTCTGTTATACATATG

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 19
------------gtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataaaatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
            | | |    ||   || |  || | |  ||||| |   |   | |  ||     | |  ||| |   |   ||| | | ||     ||  |||| || ||  | || || ||||| |||||||| ||||| || ||||| |||||||||||||| ||||| ||| |||| ||||||||||||||||| ||||
ctcaagatcttggaaagtggaaagcttctagctacctgagaatataaatctaaacctctctgatttgcttcaattatggttcctgtttctcttc----atgcagGGTACGAGTCGTCCAGCTCATTATCATGTTCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTTTGACAAACAATCTCTGTTATACATATG

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 20
gtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataa---------aatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
   |  |  ||   || | || | | ||| ||  | |||      | ||| ||   | |         ||  |  |    | | ||| |  ||| ||  |||| || ||  |||| || ||||| ||||| || ||||| || ||||| |||||||||||||| ||||| |||||||| |||||||| |||||||| ||||
-cccagagtaaaattctagatctgctttactagtatcttagaaaaatctaaacctttgatttttccttaactatgcatactttttttatattatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 17
----------gtacgaaacaactatcgaaatatccgttaatatgacct-tttccgtaactatacagataaa-atgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
           || ||  |    ||       |   | | ||  |  |  || |  |||| |    ||  |   | || | |||   ||  ||||       |||| ||||| |||||||| |||||||||||| | ||||| ||||||||||||||||||||||| ||||||||  |||| |||||||| || || || ||||
aacactcactttaggaggctctcatttgtcagtttctaactaacatgtgctttcagaacttttggaatggatgagtcattattttctttctttgtgg----cagGGGACAAGTAGGCCTGCTCATTACCATGTTTTATGGGATGAGAACAATTTCACAGCAGATGGAATTCAATCCTTGACGAACAATCTTTGCTACACATATG

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: EFJ19863 (Selaginella moellendorffii), 3'ss of exon 18
gtacgaaacaactatcgaaatatccgttaatatgacctt---ttccgtaactatacagataaaatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
                      |   || ||    || |    |  ||| || | |  |||  | || |||               ||| |  ||||||||||||| || ||||| || || || ||||||||||||||||| ||||| || |||||  | || || || || ||||  || || || || || |
---------------------gtaacttgatggagccctggcctttgtagctttgctcatacgacgagact---------------atgttacagGGAACAAGCAGACCAGCACACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|164068023|gb|ES138854.1|ES138854
EST:     GCCATGCGGGTATTCAG                         GGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTA
genomic: GCCATGCGGGTATTCAGgtacgaaaca ... tatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTT-
EST: gi|124716615|gb|EH808017.1|EH808017
EST:     ATGCGGGTATTCAG                         GGAACAAGCAGGCCTGCGCATTACCATGTTCTTTGGGACGAGAACAATTTC
genomic: ATGCGGGTATTCAGgtacgaaaca ... tatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTC
EST: gi|164006274|gb|ES130508.1|ES130508
EST:     GCCATGCGGGTATTCAG                         GGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATT-C
genomic: GCCATGCGGGTATTCAGgtacgaaaca ... tatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccgtaactatacagataaaatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG
    ccgtaac  putative branch site (score: 3)
           tatacagataaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataaaatgacactgtttgtgtttgttgtatgatctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG