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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctaattcttaatgactgcttgcaagttactttgtgcaatctaactgaactttttcctggtgcagATTGCTCAAAGGAATAGCTTAGACGTGGATGTTGACTTAGCCCTTGGTTTTGCCTCGCATTATAGTAAAATCGAAACGATGGATTGCCTTGTAGAAGAAG

Basic information

species Arabidopsis thaliana
transcript AT2G44090.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44090.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G40370.1 (Glycine max), 3'ss of exon 3
-------------------------------gtaaatctaatt-cttaatgactgcttgcaagttactttgtgcaatctaactgaactttttcctggtgcagATTGCTCAAAGGAATAGCTTAGACGTGGATGTTGACTTAGCCCTTGGTTTTGCCTCGCATTATAGTAAAATCGAAACGATGGATTGCCTTGTAGAAGAAG
                                || ||   ||    |  |||    ||         |||||| |   |    | | |    |    |||||||||||||||| || ||||| || || ||||||||||| ||  | ||||||||||| |||||| | || || | ||| ||||| ||| | || ||||| |
gtgtatgaagtgaggtagtgaatttctgtttatatattatatagtctgctgaaaatttttggtcatgtttgtgtaccatgctgggaatcaaact--atgcagATTGCTCAAAGAAACAGCTTGGATGTTGATGTTGACTTGGCGTTGGGTTTTGCCTCCCATTATGGCAAGATAGGAACTATGGAATGCTTGGTGGAAGAGG

upper sequence: AT2G44090.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G00260.1 (Glycine max), 3'ss of exon 2
------------------------------gtaaatc-taattcttaatgactgcttgcaagttac-tttgtgcaatctaactgaactttttcctggtgcagATTGCTCAAAGGAATAGCTTAGACGTGGATGTTGACTTAGCCCTTGGTTTTGCCTCGCATTATAGTAAAATCGAAACGATGGATTGCCTTGTAGAAGAAG
                               || ||  ||     |  |||    ||     | |  |||||| |   |  |||    |    ||  |||||||||||||||| || ||||| || || ||||||||||| ||  | ||||||||||| |||||| | || || | ||| ||||| ||| | || ||||| |
cttgtgaagtgatgtagtgaattgctgtttatatattatatagtctgctgaaaatttttggttcatatttgtgtaccatg-ctgtgaatcaaacta-tgcagATTGCTCAAAGAAACAGCTTGGATGTTGATGTTGACTTGGCGTTGGGTTTTGCCTCCCATTATGGCAAGATAGGAACTATGGAGTGCTTGGTGGAAGAGG
















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|125186415|gb|EL201369.1|EL201369
EST:     TTGAAGCTTCTCGTTTTGGGAGCACAGAACTTGTGCGCATCTTGTTGCAG                         ATTGCTCAAAGGAATA
genomic: TTGAAGCTTCTCGTTTTGGGAGCACAGAACTTGTGCGCATCTTGTTGCAGgtaaatctaa ... cctggtgcagATTGCTCAAAGGAATA
EST: gi|86087288|gb|DR383047.1|DR383047
EST:     TTGAAGCTTCTCGTTTTGGGAGCACAGAACTTGTGCGCATCTTGTTGCAG                         ATTGCTCAAAGGAATAGCTTAGACGTGGATGTTGACTTAGCCCTTGGTTTT
genomic: TTGAAGCTTCTCGTTTTGGGAGCACAGAACTTGTGCGCATCTTGTTGCAGgtaaatctaa ... cctggtgcagATTGCTCAAAGGAATAGCTTAGACGTGGATGTTGACTTAGCCCTTGGTTTT
EST: gi|124715640|gb|EH807042.1|EH807042
EST:     TTGAAGCTTCTCGTTTTGGGAGCACAGAACTTGTGCGCATCTTGTTGCAG                         ATTGCTCAAAAGGAATA
genomic: TTGAAGCTTCTCGTTTTGGGAGCACAGAACTTGTGCGCATCTTGTTGCAGgtaaatctaa ... cctggtgcagATTGCTCAAA-GGAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgactgcttgcaagttactttgtgcaatctaactgaactttttcctggtgcagATTGCTCAAAGGAATAGCTTAGACGTGGATGTTGACTTAGCCCTTGGTTTTGCCTCGCATTATAGTAAAATCGAAACGATGGATTGCCTTGTAGAAGAAG
                            atctaac  putative branch site (score: 2)
                                       ctttttcct  putative PPT
                                     aacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatctaattcttaatgactgcttgcaagttactttgtgcaatctaactgaactttttcctggtgcagATTGCTCAAAGGAATAGCTTAGACGTGGATGTTGACTTAGCCCTTGGTTTTGCCTCGCATTATAGTAAAATCGAAACGATGGATTGCCTTGTAGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG