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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACGGCTACACCTTGAGGATGTTCTGCATCGCCTTCACAAAGAGACGTGCTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAGgttacaacattatcataccatgtgcttactatttggctttctgtaaacagaagattaacattttccttgtaaatgtttcttgattcttgtag

Basic information

species Arabidopsis thaliana
transcript AT4G34670.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA11G00890.1 (Glycine max), 5'ss of exon 4
AGACGGCTACACCTTGAGGATGTTCTGCATCGCCTTCACAAAGAGACGTGCTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAGgt--------tacaacattatcataccatgtgcttactatttggctttctgtaaacagaagattaacattttccttgtaaatgtttcttgattcttgtag-
 ||    || || ||||||||||||||||| | ||| || ||||| |||  |||||| |||||| | |||||||| || ||||| ||||||||| | |||||        | ||||||| | ||   || || || | || |    ||    | | |   |        | |  |   | ||  || | |    ||| |  
TGATAATTATACATTGAGGATGTTCTGCATTGGCTTTACTAAGAGGCGTAGTAACCAGGTGAAGAGGACCTGTTATGCACAATCGAGCCAAATCAGACAGgtatagttactgcaacattcttat-tgatttgttttcaatctattctttcaaatatactgggactgggatatgttccaacattcttatggtaatttgaacc

upper sequence: AT4G34670.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv14s0030g01810.t01 (Vitis vinifera), 5'ss of exon 5
AGACGGCTACACCTTGAGGATGTTCTGCATCGCCTTCACAAAGAGACGTGCTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAGgttacaacattatcataccatgtgcttactatttggctttctgtaaacagaagattaacattttccttgtaaatgtttct--tgattcttgtag------
|||   ||||||| |||||||||||||||| || ||||||||||  |||   |||||    |||   || |  || || |||||||| || ||||||||||||      ||   || ||||     | |||| |   || ||         |  ||   ||  | ||  ||||   | ||  |  ||||| ||       
AGATAACTACACCCTGAGGATGTTCTGCATTGCATTCACAAAGAAGCGTCAAAACCAGAACAAGAAAACTTCATATGCCCAATCCAGTCAGATCCGTCAGgttta---gttggaattccattcaacttctatct--tttccttgtggtttgactttgcaatggtactgataaagaatgctggtacttcttttaatggcag
















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|125255400|gb|EL269485.1|EL269485
EST:     CTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGAAAGATGAGTGAGATTATGG
genomic: CTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAGgttacaacat ... attcttgtagATCCGCAGAAAGATGAGTGAGATTATGG
EST: gi|47829184|gb|CK118868.1|CK118868
EST:     CTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGAAAGATGAGTGAGATTATGGTGAAGGAGGCTTCATCTTGTGAC
genomic: CTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAGgttacaacat ... attcttgtagATCCGCAGAAAGATGAGTGAGATTATGGTGAAGGAGGCTTCATCTTGTGAC
EST: gi|125184008|gb|EL198962.1|EL198962
EST:     CTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGAAAGATGAGTGAGATTATGGTGAAGGAGGCTTCAT
genomic: CTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAGgttacaacat ... attcttgtagATCCGCAGAAAGATGAGTGAGATTATGGTGAAGGAGGCTTCAT
EST: gi|164020797|gb|ES108567.1|ES108567
EST:     CTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGAAAGATGAGTG
genomic: CTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAGgttacaacat ... attcttgtagATCCGCAGAAAGATGAGTG
EST: gi|125248519|gb|EL262604.1|EL262604
EST:     GTTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGAAAGATGAGTGAGATTATGGTGAAGGAGGCTTCATCTTGTGAC
genomic: GTTACGCTCAATCCAGCCAAATCCGTCAGgttacaacat ... attcttgtagATCCGCAGAAAGATGAGTGAGATTATGGTGAAGGAGGCTTCATCTTGTGAC
EST: gi|164033173|gb|ES109127.1|ES109127
EST:     CAAATCCGTCAG                         ATCCGCAGAAAGATGGAGTGAGATTATGGTGAAGGAGGCTTCATCTTGTGA
genomic: CAAATCCGTCAGgttacaacat ... attcttgtagATCCGCAGAAAGAT-GAGTGAGATTATGGTGAAGGAGGCTTCATCTTGTGA
EST: gi|164206383|gb|ES090331.1|ES090331
EST:     CCAAGTGAAGCGTACCTGTTACGCCCAATCCAGCCAAATCCGTCAG                         ATCCGCAGAAAGATGAGTGAGATTATGGTGAAGGAGGCTTCATCTTGTGAC
genomic: CCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAGgttacaacat ... attcttgtagATCCGCAGAAAGATGAGTGAGATTATGGTGAAGGAGGCTTCATCTTGTGAC
EST: gi|86059960|gb|DR355717.1|DR355717
EST:     CTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAG                         ATCCGCAGAAAGATGAGTGAGATTATGGTGAAGGAGGCTTCATCTTGTGAC
genomic: CTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAGgttacaacat ... attcttgtagATCCGCAGAAAGATGAGTGAGATTATGGTGAAGGAGGCTTCATCTTGTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACGGCTACACCTTGAGGATGTTCTGCATCGCCTTCACAAAGAGACGTGCTAACCAAGTGAAGCGTACCTGTTACGCTCAATCCAGCCAAATCCGTCAGgttacaacattatcataccatgtgcttactatttggctttctgtaaacagaagattaacattttccttgtaaatgtttcttgattcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC