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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatatctctttcaaaatatgatctgtatttttctttcaggtgatataaatggaaggaagtatcgtgaccggttgttgttataacttatatgtggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGA

Basic information

species Arabidopsis thaliana
transcript AT4G14030.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G36670.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------------------gtaacatatctct---ttcaaaatatgatctgtatttttctttcaggtgatataaatggaaggaagtatcgtgaccggttgttgttataacttatatg---tggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGA
                                                                                          || |  || || |   |  |  |  |  |      ||| || ||   ||   ||| ||  |   | | |    |   |   |  |||||||| || |    |   ||||||| || ||||||||||||||  ||||||||||||| ||||| |||||||| ||| | ||||| |||||| ||||||| |||| |   |||||| ||||||
gcaagttgttaacataatccagggagatgtttagaatgcattaattttattcttttaactttgtgtatttgaagcctgtttattacccctgtgatttaactatgactgtactaagtacttccccctttcctctcgcttgtagtaattgtgaaccaatttgcaaaattgccat-attataactaatgtaccctaaatgcagATAAGGTTCTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGGAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGA

upper sequence: AT4G14030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G28400.1 (Glycine max), 3'ss of exon 4
gtaacatatctctttcaaaatatgatctgtatttttctttcaggtgatataaatggaaggaagtatcgtgaccggttgttgttataacttatatgtggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGA
   |  | | || ||    | ||  | | | | |  |||  |  ||  |   ||     |||   | | ||    ||||      ||||| |  |   | |||| | |||||  |||||||||| |||||||||||||| || |||||| |||| ||||| ||||| ||| || | ||||||||||     |||||| ||||||
aatatgtttgtcctttgctacattttttctctctagcttgtacttgtgaagtattatgtgaaaggt-gagataatttgtaa--gcaacttgtccgaaat-gcagGTAAGATTTCTGCATGATCCTTCTAAAGATACAGGTTTCGTTGGGTGTGCATTGTCAAGTAACATGGTACGCTTTTTCAAGACTGAAGATGAATCATGGA

upper sequence: AT4G14030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G00590.1 (Glycine max), 3'ss of exon 4
gtaacatatctctttcaaaatatgatctgtatttttctttcaggtgatataaatg-gaaggaagtatcgtgaccggttgttgttataacttatatg---tggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGA
      |  || |   ||  ||   ||     ||| || ||   ||   ||| || |||  || |  |   |  |     | |||||||| || |    |   ||||||| || || |||||||||||  ||||||||||||| ||||| || ||||| ||| | ||||| |||||| ||||||| |||| |   |||||| ||||||
------tgactgtactaag-tactttcccc-ctttcctctcgcttgtggtaattgtgaaccaatttgcaaaattgcaatattttataactgatgtaccctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGA

upper sequence: AT4G14030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------------gtaacatatctctttcaaaatatgatctgtatttttctttcaggtgatataaatggaaggaagtatcgtgaccggttgttgttataacttatatgt---ggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGA
                                                                             | | | || | |||     | || |   | ||||   |  ||    ||    || |   |  | |       ||      || |||   |  |||      ||||| | || ||  |||||||||| |||||||||||||| || || ||| |||| ||||| ||||| ||| || | |||||||||| |   |||||| ||||||
gtacattgcttaataaataattctggagttatttccaccaattataagcactttatgttaatgtacttgtgatttaatcataaatatgttt-gtcctttgctacattttttctctctagcctgtacttgtgaagtaatatgttaaaggtggcataatttgtaagcaacttgtcctaaatgcagGTAAGGTTTCTGCATGATCCTTCTAAAGATACAGGTTTCGTGGGGTGTGCATTGTCAAGTAACATGGTACGGTTTTTCAAGACCGAGGATGAATCATGGA

upper sequence: AT4G14030.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------gtaacatatctctttcaaaatatgat-----ctgtatttttctttcaggtg----atataaatggaaggaagtatcgtgaccggttgttgt-------tataacttatatgt-----ggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGA
                            |       | |   | || | ||        ||  |||||| | ||   |     || | | |   |  |  | |  | || | ||  | |       | || |||  || |     | |||||||| |||||| |||||||||| |||||||||||||||||||| ||  |||||||  | || || ||| |  |||||||||||| |   ||||   ||||||
gtgagttttggaaatataatccaccattgctttgctttttggttaagaaatagcaaatgctacatttttttctctaattttgcatgttattatgaccatatgtgttaacggtttactatctacatgtgtatcttcaatctttcttgcttgcagATAAGATTCCTGCATGATCCTTCTAAAGATACAGGGTTTGTAGGTTGTGCCTTAACAAGCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGA

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|124777875|gb|EH867818.1|EH867818
EST:     ATTGACCTTGGACCGACTGGTCTCTTACCTTTGGAG                         ATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCC
genomic: ATTGACCTTGGACCGACTGGTCTCTTACCTTTGGAGgtaacatatc ... gtggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCC
EST: gi|164102871|gb|ES158992.1|ES158992
EST:     AAATGAAACAATTAATTGACCTTGGACCGACTGGTCTCTTACCTTTGGAG                         ATTAGATTCTTGCATGATCCGTCTAAAGATACAGGGTTTGTTGGGAGTGCC
genomic: AAATAAAACAATTAATTGACCTTGGACCGACTGGTCTCTTACCTTTGGAGgtaacatatc ... gtggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCC
EST: gi|125069767|gb|EL135427.1|EL135427
EST:     AATAAAACAATTAATTGACCTTGGACCGACTGGTCTACTTACCTTTGGAG                         ATTAGATTCTTGCATGATCCAT
genomic: AATAAAACAATTAATTGACCTTGGACCGACTGGTCT-CTTACCTTTGGAGgtaacatatc ... gtggttgcagATTAGATTCTTGCATGATCCAT
EST: gi|125217694|gb|EL231777.1|EL231777
EST:     ACCGACTGGTCTCTTACCTTTGGAG                         ATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCC
genomic: ACCGACTGGTCTCTTACCTTTGGAGgtaacatatc ... gtggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCC
EST: gi|125275875|gb|EL289960.1|EL289960
EST:     TCTCTTACCTTTGGAG                         ATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCC
genomic: TCTCTTACCTTTGGAGgtaacatatc ... gtggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCC
EST: gi|47831973|gb|CK121657.1|CK121657
EST:     AAATAAAACAATTAATTGACCTTGGACCGACTGGTCTCTTACCTTTGGAG                         ATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCC
genomic: AAATAAAACAATTAATTGACCTTGGACCGACTGGTCTCTTACCTTTGGAGgtaacatatc ... gtggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCC
EST: gi|125082851|gb|EL143619.1|EL143619
EST:     AAAACAATTAATTGACCTTGGACCGACTGGTCTCTTACCTTTGGAG                         ATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCC
genomic: AAAACAATTAATTGACCTTGGACCGACTGGTCTCTTACCTTTGGAGgtaacatatc ... gtggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCC
EST: gi|125070108|gb|EL135644.1|EL135644
EST:     AAATAAAACAATTAATTGACCTTGGACCGACTGGTCTCTTACCTTTGGAG                         ATTAGATTCTTGCATGATCCATCTAAAGATACAGGG
genomic: AAATAAAACAATTAATTGACCTTGGACCGACTGGTCTCTTACCTTTGGAGgtaacatatc ... gtggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatggaaggaagtatcgtgaccggttgttgttataacttatatgtggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGA
                                ttataac  putative branch site (score: 2)
                             ttgttataacttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatatctctttcaaaatatgatctgtatttttctttcaggtgatataaatggaaggaagtatcgtgaccggttgttgttataacttatatgtggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA