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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAAGTGCTGAGGTTTGGGATGAGTCGTCGCTGGAGGCTCCCTTTTGAGTTCATAAAGgtaagtcaacggaaaaccgtagtgtctagaagataaaactagtggaaaaggattagaaaaaaaagaaactgaaaaaactttgatgttgatgcttgtgcaaatgttattatttcataatataacttaatcatgcag

Basic information

species Arabidopsis thaliana
transcript AT5G28900.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 5'ss of exon 12
--------ATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAAGTGCTGAGGTTTGGGATGAGTCGTCGCTGGAGGCTCCCTTTTGAGTT-CATAAAGgtaagtcaacggaaaaccgtagtgtctagaagataaaactagtggaaaaggattagaaaaaaaagaaactgaaaaaactttgatgtt-gatgcttgtgcaaatgttattatttcataatataacttaatcatgcag
        |||||  | || ||||||||||||| ||||||||| || |||||||||| ||| || |||||||| |||   || || ||||| ||||||  |   | |  ||   ||   |     | || || | || | |  |  | |  |  | |         || |  | ||  ||  | || || ||| || ||| ||  |                                       
GAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAAGTGGTGATGTGTGGGATGAATCG---CTTGAAGCTCCATTTTGAAATATgtgagtgttcctctctg-----ctgttgtttgtaaatggaaccatttatctatataataacttaataccaaaatttgtcagaatttagatttttgattctgatct-------------------------------------

upper sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA10G30930.3 (Glycine max), 5'ss of exon 12
--ATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAAGTGCTGAGGTTTGGGATGAGTCGTCGCTGGAGGCTCCCTTTTGAGTTCATAAA-Ggtaagt-----caacggaaaaccgta---------------gtgtctagaagataaaactagt------ggaaaaggattagaaaaaaaagaaactgaaaaaactttgatgttgatgcttgtgcaaatgttattatttcataatataactt--aatcatgcag---------------------------
  |||||||| ||||||||||||||||| |||||||| |||||||||||||| || || |||||||| ||    || ||||||||||| | |    ||    |||||||       |   || ||  |                 ||  |||||| |  |  || |        ||| | ||||   ||      | ||      |||    |||  || |   |||     | ||| ||  | | || |||||  || | ||                              
ATATTAGGCTTTCAATGGAAGAAGATGTAGAAGATGCCTCTAATGGAAGTGCAGAAGTCTGGGATGAATCA---CTAGAGGCTCCCTTCTAAAGATATTTTTGgtaagtgtttttgaaacaagacttttttctgagcctgctacatgcttagaagtttgatttattttactcaaaaatgaattaaggaagttgagatctctgttcactgcagtgtctattccc-tgctttcttcatttttaaaaattaaaacttctaaacttgtcttattttgggcattatatattagtacag

upper sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA10G30930.1 (Glycine max), 5'ss of exon 12
--ATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAAGTGCTGAGGTTTGGGATGAGTCGTCGCTGGAGGCTCCCTTTTGAGTTCATAAA-Ggtaagt-----caacggaaaaccgta---------------gtgtctagaagataaaactagt------ggaaaaggattagaaaaaaaagaaactgaaaaaactttgatgttgatgcttgtgcaaatgttattatttcataatataactt--aatcatgcag----------------------
  |||||||| ||||||||||||||||| |||||||| |||||||||||||| || || |||||||| ||    || ||||||||||| | |    ||    |||||||       |   || ||  |                 ||  |||||| |  |  || |        ||| | ||||   ||      | ||      |||    |||  || |   |||     | ||| ||  | | || |||||  || | ||                         
ATATTAGGCTTTCAATGGAAGAAGATGTAGAAGATGCCTCTAATGGAAGTGCAGAAGTCTGGGATGAATCA---CTAGAGGCTCCCTTCTAAAGATATTTTTGgtaagtgtttttgaaacaagacttttttctgagcctgctacatgcttagaagtttgatttattttactcaaaaatgaattaaggaagttgagatctctgttcactgcagtgtctattccc-tgctttcttcatttttaaaaattaaaacttctaaacttgtcttattttgggcattatatattag

upper sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA19G43790.1 (Glycine max), 5'ss of exon 11
---ATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAAGTGCTGAGGTTTGGGATGAGTCGTCGCTGGAGGCTCCCTTTTGAGTTCATAAAGgtaagtcaacggaaaaccgtagtgtctaga--agataaaactagtggaaaaggattagaaaaaaaagaaactgaaaaaactttgatgttgatgcttgtgcaaatgttattatttcataatataacttaatcatgcag
   |||||||| ||||||||||||||||| || ||||| ||||| || ||||| || ||||||||||| ||    || ||||||||||| |||  ||||  | ||||||     ||||   || || | ||    |  |  |  |||     |  | | ||||| | | |    |  |||    || | | ||  |  |    || ||  || |                          
TATATTAGGCTTTCAATGGAAGAAGATGTAGAGGATGCCTCTAACGGTAGTGCAGAAGTTTGGGATGAATCA---CTAGAGGCTCCCTTCTGACATCATTTATgtaagtt----gaaatatgtggtatataatccaattttacttagcatttatagttcagaaatagaggctttttcaaa----ttcaggctg--ggctaaataagtg--atcaa-------------------------

upper sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 12
---ATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAAGTGCTGAGGTTTGGGATGAGTCGTCGCTGGAGGCTCCCTTTTGAGTTCATAAAGgtaagtcaacggaaaaccgtagtgtctaga--agataaaactagtggaaaaggattagaaaaaaaagaaactgaaaaaactttgatgttgatgcttgtgcaaatgttattatttcataatataacttaatcatgcag
   |||||||| || |||||||||||||| || ||||| ||||| || ||||| || ||||||||||| ||    || ||||||||||| |||  ||||  | ||||||     ||||   || || | ||    |  |  |  | |     |    | ||||| | | |    |  |||    || | ||||  ||||    || ||  || |                          
TATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTAGTGCAGAAGTTTGGGATGAATCA---CTAGAGGCTCCCTTCTGACGTCATTTATgtaagtt----gaaatatgtggtatataatccaattttactttgcatttataattcagaaatagaggctttttcaaa----ttcaggttgg-gctta-ataagtgg-atca--------------------------

upper sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA20G36530.1 (Glycine max), 5'ss of exon 12
--ATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAAGTGCTGAGGTTTGGGATGAGTCGTCGCTGGAGGCTCCCTTTTGAGTTCATAAA-Ggtaagtcaacggaaaaccgtagtgtct--agaagataaaactagtggaaaag---gattagaaaaaaaagaaactgaa---aaaactttgatgttgatgcttg-tgcaaatgttattatttcataatataacttaatcatgcag---------------------------------
  |||||||| ||||||||||||||  | |||||||| ||||| |||||||| || || |||||||| ||    || ||||||||||| | |    ||     ||||||       |||    | | |||   ||   |   ||  |   | |||   ||||      |    ||| ||||   |  |  |||| ||   || |   ||||      ||| |  | |    | | ||  | |  |                                   
ATATTAGGCTTTCAATGGAAGAAGACATAGAAGATGCCTCTAACGGAAGTGCAGAAGTCTGGGATGAATCA---CTAGAGGCTCCCTTCTAAAGATATTTTCAgtaagtgtttttgaaatgagactttcttctgagactgctacatgcttagaagtttgatttattttactcaaaaatgaattcaggaagttgaggtctctgttcactgcactgtccattctcccctttcttcattttttaaaactctaaacttatcttattttgggcattctatattag

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|125323831|gb|EL337911.1|EL337911
EST:     GAGGTTTTGGGATGAGTCGTCGCTGGAGGCTCCCTTTTGAGTTCATAAAG                         AAGAGAAATGTAAAGTCCC
genomic: GAGG-TTTGGGATGAGTCGTCGCTGGAGGCTCCCTTTTGAGTTCATAAAGgtaagtcaac ... aatcatgcagAAGAGAAATGTAAAGTCCC
EST: gi|125133363|gb|EL174882.1|EL174882
EST:     TGAGTTCATAAAG                         AAGAGAAATGTAAAGTCCCTGAGAAGAACATTTGGAGCTTTGTTGAGGAAG
genomic: TGAGTTCATAAAGgtaagtcaac ... aatcatgcagAAGAGAAATGTAAAGTCCCTGAGAAGAACATTTGGAGCTTTGTTGAGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAAGTGCTGAGGTTTGGGATGAGTCGTCGCTGGAGGCTCCCTTTTGAGTTCATAAAGgtaagtcaacggaaaaccgtagtgtctagaagataaaactagtggaaaaggattagaaaaaaaagaaactgaaaaaactttgatgttgatgcttgtgcaaatgttattatttcataatataacttaatcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG