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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttgtcattgtaaaaaaatagaatctactacttttaaaccgattaatataattgttcttcttaactgatgattaattttatttcatgacttctcagGTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTCGATGAAAATGGTTTGTGGAAGAAGAAGCTCACCGAGCAATCCCTGAAGC

Basic information

species Arabidopsis thaliana
transcript AT1G12000.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 9
----------------gtgtgttgtcattgtaaaaaaatagaatctact---acttttaaac---cgattaatataattgttcttcttaactgatgattaattttatttcatgacttct---cagGTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTCGATGAAAATGGTTTGTGGAAGAAGAAGCTCACCGAGCAATCCCTGAAGC
                ||   | ||  || |      |||  || |  |   |  | |  ||   | || |||||       | | |||| ||||| | | |||||| |  |   || |   ||||||||| | || ||||| ||||| |||||||||||||||||||| | ||| |||||    ||  | ||||||||||| |||||||| || ||  | ||||
gtagctatcactagttgtcaatagtttttttctccccatatgatgttttggcatctgttcacgtacaatcaatatggaaacacctattaa-tgatggtcacttttatattcttttttgtttgcagGTCCAACACCTTATTGCAGAACTCAATGAAATTCTGGCAAATGACGCTGTGGATGAGGGAGGGCTATGGAAGAAGAAACTCACCGATCAGTCATTAAAGC
















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|124798452|gb|EH888131.1|EH888131
EST:     TACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAG                         GTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTC
genomic: TACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtc ... gacttctcagGTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTC
EST: gi|164119733|gb|ES032715.1|ES032715
EST:     ACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAG                         GTCCAAGAGCTCATT
genomic: ACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtc ... gacttctcagGTCCAAGAGCTCATT
EST: gi|125044797|gb|EL117066.1|EL117066
EST:     CTGATTCCAGAAGGTCTGATCGACTTTTATTCCTGAG                         GTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTC
genomic: CTGATTCCAGAAGGTCTGATCGAC-TTTATTCCTGAGgtgtgttgtc ... gacttctcagGTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTC
EST: gi|116438054|gb|EG480646.1|EG480646
EST:     ACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAG                         GTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTC
genomic: ACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtc ... gacttctcagGTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTC
EST: gi|125316880|gb|EL330965.1|EL330965
EST:     ACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAG                         GTCCAAGAGCT
genomic: ACTACGGTGTCATACTGATTCCAGAAGGTCTGATCGACTTTATTCCTGAGgtgtgttgtc ... gacttctcagGTCCAAGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaatataattgttcttcttaactgatgattaattttatttcatgacttctcagGTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTCGATGAAAATGGTTTGTGGAAGAAGAAGCTCACCGAGCAATCCCTGAAGC
                                               cttctc  CT-rich tract
                   ttaactgatgattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttgtcattgtaaaaaaatagaatctactacttttaaaccgattaatataattgttcttcttaactgatgattaattttatttcatgacttctcagGTCCAAGAGCTCATTGCTGAACTGAATGAAATTCTGGCAAATGAGGTTGTCGATGAAAATGGTTTGTGGAAGAAGAAGCTCACCGAGCAATCCCTGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC