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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcctcttcctcttctagacttgcaaggtttctgaacattagcttttaaaagaacactgttctcactctgtttgtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCAGGACTACCTGAAGGTGGTGTTTTGCTCTTGGAGAATGTGAGGTTCTACG

Basic information

species Arabidopsis thaliana
transcript AT1G79550.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 3
---------------gtttgttcctcttcctcttctagacttgcaaggtttctgaac-attag--cttttaaaagaacactgttctcactctgtttgtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCAGGACTACCTGAAGGTGGTGTTTTGCTCTTGGAGAATGTGAGGTTCTACG
                |   |     ||  | ||||  | ||        |   |||   |||  | | | | |   |  |||| | |   |||   |||   |||||||| ||||| |||||||  || ||||||||||||||||| |||| |||     |||| || ||||||||| ||||  | || |||||  |||||||| 
gtatgctataaaaggataaatcatatttattattctgcaattctgcttactacaaactggtagaccatcttatatttccatgttttgatgatgtccttgtcg-tagGTTGTGATGGCCAATGACTGCATCGGTGAGGAAGTCCAGAAATTGGCTGCCACTTTACCAGATGGTGGTGTTCTGCTTCTAGAAAATGTTCGGTTCTACA

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G17600.1 (Glycine max), 3'ss of exon 3
---------------------gtttgttcctcttcctcttctagacttgcaaggtttctgaacattagcttttaaaagaacactgttctcactctg--tttgtgttaata--gGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCAGGACTACCTGAAGGTGGTGTTTTGCTCTTGGAGAATGTGAGGTTCTACG
                      |||| |  | ||    ||    | |    |    ||      ||   |  |  |   || || |  ||| | |   ||| | || |||  ||||   |||||||||||||||||||| ||||||||  ||||||||||||||  ||| || |||||||||||||||||  | |||||||||||||||||  
gtgtgccttataaacttctctatttggttttgttttgttttggcattcctgacacctcct--tttttattgctggatttactctttattcattgtcattttctcttgatatagGTTACGATGGCAAATGACTCTATTGGGGAGGAAGTTGAGAAGTTGGTTGCACAACTTCCAGAAGGTGGTGTTTTGCTTCTAGAGAATGTGAGGTTCTATA

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G41550.1 (Glycine max), 3'ss of exon 3
----------------------gtttgttcctcttcctc-ttctagacttgcaaggtttctgaacattagcttttaaaagaacactgttctcactctgtttgtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCAGGACTACCTGAAGGTGGTGTTTTGCTCTTGGAGAATGTGAGGTTCTACG
                       ||||||    ||   | |||    |   |    ||  |   | | |  || |       ||||||  ||| | | | | || | | |||||   ||||| |||||||||||||| ||||||||  | ||||||||| ||  ||| || |||||||||||||||||  | |||||||||||||||||| 
gtgtgccttctaagctgctccattttgttttgttttggcattccttccacccccttttcgtttgcttgattttctgcttattcactgtg-tcattttctct-tgattacagGTTACGATGGCCAATGACTCTATTGGGGAGGAAGTTGAAAAGTTGGTTACACAACTTCCAGAAGGTGGTGTTTTGCTTCTAGAGAATGTGAGGTTCTACA

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 3'ss of exon 2
gtttgttcctcttcctcttctagacttgcaaggtttctgaacattagcttttaaaagaacactgttctcactc------------tgtttgtgttaa-tagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCAGGACTACCTGAAGGTGGTGTTTTGCTCTTGGAGAATGTGAGGTTCTACG
|||||||  |   |   |  |    |||    |||  | ||   |   ||       |  | ||| ||||||             ||||||  || | ||||||  |||||||||||| | |||||||||||||||| |||  ||||| ||   | |||| |||||||| ||| | ||| | |||||||||||||| ||| 
gtttgtttattccctaatatttctgttgttttgttattcaaacctgatttggctggcatgaatgtactcacttggatgacttttttgtttgcctttactagGTTAAAATGGCAAATGATTGTATTGGTGAGGAAGTCAAGATATTGGTGGCTAAAATACCAGAAGGTGGGGTTCTCCTCCTTGAGAATGTGAGGTTTTACA

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|47828512|gb|CK118196.1|CK118196
EST:     ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG                         GTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
genomic: ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAGgtttgttcct ... gtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
EST: gi|116446998|gb|EG489590.1|EG489590
EST:     ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG                         GTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
genomic: ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAGgtttgttcct ... gtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
EST: gi|47831797|gb|CK121481.1|CK121481
EST:     ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG                         GTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
genomic: ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAGgtttgttcct ... gtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
EST: gi|47829445|gb|CK119129.1|CK119129
EST:     ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG                         GTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
genomic: ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAGgtttgttcct ... gtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
EST: gi|116434727|gb|EG477319.1|EG477319
EST:     ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG                         GTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
genomic: ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAGgtttgttcct ... gtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
EST: gi|116403251|gb|EG445843.1|EG445843
EST:     ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG                         GTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
genomic: ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAGgtttgttcct ... gtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
EST: gi|47831355|gb|CK121039.1|CK121039
EST:     ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG                         GTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
genomic: ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAGgtttgttcct ... gtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
EST: gi|47828442|gb|CK118126.1|CK118126
EST:     ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG                         GTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
genomic: ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAGgtttgttcct ... gtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
EST: gi|116434726|gb|EG477318.1|EG477318
EST:     ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG                         GTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
genomic: ACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAGgtttgttcct ... gtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
EST: gi|47828962|gb|CK118646.1|CK118646
EST:     GATTGTCTGAACTTCTTGGTGTTGAG                         GTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA
genomic: GATTGTCTGAACTTCTTGGTGTTGAGgtttgttcct ... gtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgaacattagcttttaaaagaacactgttctcactctgtttgtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCAGGACTACCTGAAGGTGGTGTTTTGCTCTTGGAGAATGTGAGGTTCTACG
                               ttctcac  putative branch site (score: 2)
         attagcttttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttcctcttcctcttctagacttgcaaggtttctgaacattagcttttaaaagaacactgttctcactctgtttgtgttaatagGTTGTAATGGCAAATGACTCTATTGGTGAGGAAGTCCAGAAGTTGGTTGCAGGACTACCTGAAGGTGGTGTTTTGCTCTTGGAGAATGTGAGGTTCTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA