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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAGgtactcaaaatatcttaattatttatggcagctacgctgtgtcataagtatgcataatatctatcatttggtcgacag

Basic information

species Arabidopsis thaliana
transcript AT5G26830.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G26830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA01G03930.1 (Glycine max), 5'ss of exon 6
GCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAGgt-actcaaa----atatcttaattatttatggcagctacgctgtgtcataagtatgcataatatctatcatttggtcgacag-----------------
|| |||||||| || |||| ||| |||||||| || || || || || ||||||||||| ||||||||||||||||||||    |||||||| | |   |    |||| ||| || |||  |  | | |  | |      |        |    |  ||    || || |  |                 
GCTTCATCAGCATATTGGAGGGGGGACAAAGATCGGGAAAGTTTACAAAGAGTTTATGGCATATCTTATCCTGATCAGAAAAGTCTGAAGgtgattttcatttcatatgttatttctttgagtaaaccattcagctattcagactgagctgtggtggattgaatgttcaattgcagttccttgtggaatg

upper sequence: AT5G26830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA02G03750.1 (Glycine max), 5'ss of exon 6
GCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAGgtactcaaaatatcttaa-ttatttatggcagcta--cgctgtgtcata-agtatgcataata-tctatcatttggtcgacag-----------------
|| |||||||| || |||| ||| |||||||| || || || || || ||||||||||| ||||||||||||||||||||    || |||||  |    || || ||| |||||| |   ||  |  |  |  |  ||  ||  ||     |  |  ||    || || |  |                 
GCTTCATCAGCATATTGGAGGGGGGACAAAGATCGGGAAAGTTTACAAAGAGTTTATGGCATATCTTATCCTGATCAGAAAAGTCTAAAGgtgattttcatttcataagttatttctttgagtaatccattcagctattcagactgagctgtggtggattgaatgttcaattgcagttccttgtggaacg

upper sequence: AT5G26830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv19s0015g00470.t01 (Vitis vinifera), 5'ss of exon 7
GCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAGgtactcaaaatatcttaattatttatggcagctacg--ctgtgtcataagtatgcataata-tctatcatttggtcga-cag-------------------
|| ||||||||||||||||  ||  | | ||| ||||| || ||||| ||||||||||||||||| |||||||||   || |   |||||||| | |  || | |      ||| | | |  || |   | | || | | | ||     |  ||  |    | || || | |                   
GCTTCATCAGCTTACTGGAGAGGAAATAGAGATCGTGAAAGTTTGCAAAGAGTTTATGGGATATCGTATCCTGATTCAAAACGATTGAAGgtaat-atcatttttggcactttttttgtatgtatggtttatttcttcattttgttagttggtcagttgccttgttgaactgctggatatatatgtttgac

upper sequence: AT5G26830.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 5'ss of exon 7
GCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAGgtactcaaaatatcttaattatttatggcagctacgctgtgtcataagtatgcataatatctatcatttggtcgacag--------------------------
|| ||||||||||||||||  ||  | ||||| |||||||| ||||| |||||||||||||||||||||||||||   || |   |||||||| | |  || | |    | ||| |   |  || | |   | ||   |    ||    | | | | ||||||    |                          
GCTTCATCAGCTTACTGGAGAGGAAATAAAGATCGTGAGAGTTTGCAAAGAGTTTATGGGATATCTTATCCTGATTCAAAACGATTGAAGgtaat-atcatttttggccttttttttctatgtatgat---ttatttcttctgatttgctttgttagttggtcagttgtcttgttgaactgctggatatatata

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|86063891|gb|DR359648.1|DR359648
EST:     GATATCTTATCCTGATCAGAAGCAGCTGAAG                         AAATATCTCCAATTTCTAGAAGAAGCCAAAAAGTATGACCACAGACTATTG
genomic: GATATCTTATCCTGATCAGAAGCAGCTGAAGgtactcaaaa ... tggtcgacagAAATATCTCCAATTTCTAGAAGAAGCCAAAAAGTATGACCACAGACTATTG
EST: gi|164201279|gb|ES045858.1|ES045858
EST:     GCTTACAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAG                         AAATATCTCCAATTTCTAGAAGAAGCCAAAAAGTA
genomic: GCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAGgtactcaaaa ... tggtcgacagAAATATCTCCAATTTCTAGAAGAAGCCAAAAAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTCATCAGCTTACTGGAAGGGTGACAAAGACCGTGAGAGCTTGCAGAGAGTTTATGGGATATCTTATCCTGATCAGAAGCAGCTGAAGgtactcaaaatatcttaattatttatggcagctacgctgtgtcataagtatgcataatatctatcatttggtcgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG