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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaacacttatgatttatagttttgtcaataatccattcgcctaggttcttgattcttgatctaattttatctatgtattgtag

Basic information

species Arabidopsis thaliana
transcript AT4G11960.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g41460.6 (Oryza sativa), 5'ss of exon 1
---TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaacacttatgatttatagttttgtcaataatccattcgcctaggttcttgattcttgatctaattttatctatgtattgtag--------------
    | |||||||||||    || ||  | ||||| ||||| ||||| |||||||| || || ||| | ||||||||||||||||| ||||| |||||||||||     |   |  |||  |  | || |   |  | |     ||  ||  |||  |      | ||| | |   |      || |               
TAGGCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattccttttcttctagcttgtacgagatccc-ggcccttactgtacactataagtgtgcatgc-cgctgaaaagaaaaagattatt

upper sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g41460.2 (Oryza sativa), 5'ss of exon 2
TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaacacttatgatttatagttttgtcaataatccattcgcctaggttcttgattcttgatctaattttatctatgtattgtag--------------
 | |||||||||||    || ||  | ||||| ||||| ||||| |||||||| || || ||| | ||||||||||||||||| ||||| |||||||||||     |   |  |||  |  | || |   |  | |     ||  ||  |||  |      | ||| | |   |      || |               
GCCTTTTATTACGACAAGAAGGCCGTAATGTCGAATGAGGAGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattccttttcttctagcttgtacgagatccc-ggcccttactgtacactataagtgtgcatgc-cgctgaaaagaaaaagattatt

upper sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g21900.1 (Oryza sativa), 5'ss of exon 2
TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaacacttatgatttatagttttgtcaataatccattcgcctaggttcttgattcttgatctaattttatctatgtat-tgtag-----------
 | |||||||||||    || || || || || || || | ||| |||||||| || || ||| | ||||||||||||||||| ||||| |||||||||||     |   |  |||  |  | || |   |   |  |    ||  |  |     |    |   ||  ||||   || |  |  ||           
GCCTTTTATTACGACAAGAAGGCCATAATATCGAACGAGGTGTTCGATAACCTCAAGGAGGAGCTTATGTGGGAAGGAAGCAGCGTTGTGATGCTAAgtaagtggtataaaatattccttttcttctagctgtacactataactgtgcacgccgctgaaaagaaaagattattgttggaaattcagagataatccta

upper sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g64020.1 (Oryza sativa), 5'ss of exon 1
---TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaacacttatgatttatagttttgtcaataatccattcgcctaggttcttgattcttgatctaattttatctatgtattgtag-
    | || || |||||    || || || ||||| || || ||||| || ||||| || || ||| | ||||||||||| ||||| |||||||||||||||||  |  |||  |  |  ||   ||   |    | | ||  |  |||  ||||  ||    |   | |   |   || | || |   
CAGGCCTTCTACTACGACCAGAAGGCCATCATGTCCAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGCAGCAGCGTTGTCATGCTAAgtaagtactactcct--tccatctcttctgcggatacctatctgt-tagtatcttctttgcccactaattaacactaatatcttttcag

upper sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM5G885392_T01 (Zea mays), 5'ss of exon 2
TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaacacttatgatttatagttttgtcaataatccattcgcctaggttcttgattcttgatctaattttatctatgtattgtag-------------
 | || || ||||||||||| ||||| ||||| || || ||||| || ||||| || || ||| | ||||||||||| ||||| || || ||||||||| | |  |  || | | | ||        |      | | |        ||  ||  ||     |  ||  ||   | |||||                 
GCCTTCTACTACGAAGGCAAGGCGATCATGTCGAACGAGGAGTTCGACAACCTCAAGGAGGAGCTCATGTGGGAAGGGAGCAGCGTCGTGATGCTAAgtga-gtgcgtttttcactaattaagcccccctcctgcgactttttattattactgtgtcgatgacgtatactagaaacgtatttccttagacgacgacaa

upper sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 3
TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaaca--------cttatgatttatagtt----ttgtcaataa---tccattcgcctaggt-tcttgattcttgatctaattttatctatgtattgtag--
 | || ||||| || || || || || ||||| ||||||||||||||||| || || |||||  | ||||||||||||||||| ||||||||||||||||     ||        || |  |  |  || |    |||||| | |   |   ||  |   ||| | || ||  ||  |     ||| |   |  ||||||   
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAGTTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatgaggcaacttcactctcagtagctgcagctgttgttgtcattgaatttgtgttaacgcgggtgtatttatcttttttaagtctttgttggttgattgtacag

upper sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA17G14240.1 (Glycine max), 5'ss of exon 3
TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaacacttatgatttatagttttgtcaataatccattcgcctaggttcttgattcttgatctaattttatctatgtattgtag
 | || ||||| || || || || || ||||| |||||||| |||||||| || || |||||  | ||||||||||||||||| ||||||||||||||||  |  ||  |  | | |||||||    |  |  ||    |  |    || |  | |||| || |  ||   | ||          
GCATTCTATTATGAGGGAAAGGCTATCATGTCAAATGAAGAATTTGATAATCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTCATGCTAAgtatggggcaacttcgctctatagttgcagctgttgtcataacttcatctttttaaagtctttat-tggttgattgtacag-------

upper sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA01G42360.2 (Glycine max), 5'ss of exon 3
TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgta-atgaacact-----tatgatttatagttt-------tgtcaataatccattcgcctaggttcttgat----tcttgatctaattttatctatgtattgtag-------------------
 | || ||||| || || || || |||||||| ||||| || |||||||| ||||| |||||  | ||||||||||| ||||  ||||| |||||||||| || |  | |     | ||  |   | |||       || || |         || |   ||| || |    |  | |  | ||||||| | ||  |  |                     
GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAATCTTAAGGAAGAACTCATGTGGGAAGGGAGCACCGTTGTGATGCTAAgtatattattattatatatgtggctagcaatttcattcactgacagttgctagcatgcatgaattcctgctaactttgtaaattgattttatttttgagtcattataattggttcgctgtgtag

upper sequence: AT4G11960.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 3
TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaa-----tgaacacttatgatttatagttttgtcaataatccattcgcctaggttcttgattctt---gatctaattttatct---atgtattgtag
|| |||||||| || || || || |||||||| ||||| || ||||| ||||| || |||||  | ||||||||||||||||| ||||| ||||||||||      |  |   |  | ||  |||  ||| | |   |    || |      || || | |||     || |||  ||  ||    |||| || ||
TCTTTTTATTATGAGGGAAAGGCTATTATGTCAAATGAGGAATTTGACAACCTCAAGGAAGAACTCATGTGGGAAGGAAGCAGCGTTGTTATGCTAAgtacatatttagattatcttaatcaatatctttatgatataatagtttgtaatactttttaaatctctaaaatgtaaaattggcttatgtgtaatgcag

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|116378737|gb|EG421329.1|EG421329
EST:     TAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAA                         GTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTCTGGAA
genomic: TAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaaca ... tgtattgtagGTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTCTGGAA
EST: gi|124735327|gb|EH826729.1|EH826729
EST:     ATGTGGGAAGGAAGCAGTGTTGTCATGCTAA                         GTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTCTGGAA
genomic: ATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaaca ... tgtattgtagGTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTCTGGAA
EST: gi|164109880|gb|ES063212.1|ES063212
EST:     AAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAA                         GTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTC
genomic: AAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaaca ... tgtattgtagGTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTC
EST: gi|19877739|gb|AU238570.1|AU238570
EST:     TAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAA                         GTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTCTGGAA
genomic: TAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaaca ... tgtattgtagGTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTCTGGAA
EST: gi|47831512|gb|CK121196.1|CK121196
EST:     TAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAA                         GTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTCTGGAA
genomic: TAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaaca ... tgtattgtagGTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTCTGGAA
EST: gi|116378739|gb|EG421331.1|EG421331
EST:     TAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAA                         GTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTCTGGAA
genomic: TAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaaca ... tgtattgtagGTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTCTGGAA
EST: gi|124862404|gb|EH946841.1|EH946841
EST:     GCAGTGTTGTCATGCTAA                         GTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTCTGGAA
genomic: GCAGTGTTGTCATGCTAAgtaatgaaca ... tgtattgtagGTTCTGATGAACAAAGATTCCTTGAAGCTTCAATGGCTTATGTCTCTGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTTTTATTACGAAGGCAAAGCGATTATGTCTAATGAAGAGTTTGATAACCTTAAAGAAGAGTTGATGTGGGAAGGAAGCAGTGTTGTCATGCTAAgtaatgaacacttatgatttatagttttgtcaataatccattcgcctaggttcttgattcttgatctaattttatctatgtattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA