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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagaaaatgagaagctttttgacattgaatagtagagttcttgttttacatttgtcagggaaactcactgtatagatttgttgaaatgtttattatatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAG

Basic information

species Arabidopsis thaliana
transcript AT1G20260.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 3
----gtatagaaaatgagaagctttttgacattgaatagtagagttcttgttttacatttgtcagggaaactcactgtatagatttgttgaaatgtttattatatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAG
     | |      |    |  | ||     ||  |    | |||| || ||  |   | || |     || |||||    |||    | |    |  | | | |||||||||||| || ||||||||||| ||||||||| | ||||||||  ||||| |||||||||| ||||| || ||||||||||||||||||||||| |||
gtagatttgcttttttgtcatttcttctttcttctaatacaaagtttttattggagtatagtgacacctacacactgagatgatactataactcttaaactgt-tcagGGTCCAAAATATCAGGAGATTGTCAATATTCGCCTTGGAGATGGCACAACGCGACGTGGTCAAGTCTTAGAAGTTGATGGGGAGAAAGCTGTTGTGCAG
















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|116471926|gb|EG514518.1|EG514518
EST:     GAACTGTCTCCGGAGTTGCTGGACCTTTGGTCATCCTTGACAAAGTGAAG                         GGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACG
genomic: GAACTGTCTCCGGAGTTGCTGGACCTTTGGTCATCCTTGACAAAGTGAAGgtatagaaaa ... attatatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACG
EST: gi|116483049|gb|EG525641.1|EG525641
EST:     GAACTGTCTCCGGAGTTGCTGGACCTTTGGTCATCCTTGACAAAGTGAAG                         GGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACG
genomic: GAACTGTCTCCGGAGTTGCTGGACCTTTGGTCATCCTTGACAAAGTGAAGgtatagaaaa ... attatatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACG
EST: gi|164216640|gb|ES085784.1|ES085784
EST:     CTGTCTCCGGAGTTGCTGGACCTTTGGTCATCCTTGACAAAGTGAAG                         GGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACG
genomic: CTGTCTCCGGAGTTGCTGGACCTTTGGTCATCCTTGACAAAGTGAAGgtatagaaaa ... attatatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACG
EST: gi|116424900|gb|EG467492.1|EG467492
EST:     GAACTGTCTCCGGAGTTGCTGGACCTTTGGTCATCCTTGACAAAGTGAAG                         GGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACG
genomic: GAACTGTCTCCGGAGTTGCTGGACCTTTGGTCATCCTTGACAAAGTGAAGgtatagaaaa ... attatatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACG
EST: gi|152038085|gb|BP807684.2|BP807684
EST:     GAACTGTCTCCGGAGTTGCTGGACCTTTGGTCATCCTTGACAAAGTGAAG                         GGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACG
genomic: GAACTGTCTCCGGAGTTGCTGGACCTTTGGTCATCCTTGACAAAGTGAAGgtatagaaaa ... attatatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACG
EST: gi|124857653|gb|EH942090.1|EH942090
EST:     GAACTGTCTCCGGAGTTGCTGGACCTTTGGTCATCCTTGACAAAGTGAAG                         GGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAAC
genomic: GAACTGTCTCCGGAGTTGCTGGACCTTTGGTCATCCTTGACAAAGTGAAGgtatagaaaa ... attatatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatttgtcagggaaactcactgtatagatttgttgaaatgtttattatatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAG
               aactcac  putative branch site (score: 2)
                        tatagatttgttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagaaaatgagaagctttttgacattgaatagtagagttcttgttttacatttgtcagggaaactcactgtatagatttgttgaaatgtttattatatcagGGTCCAAAGTACCAGGAGATTGTTAATATTCGCTTAGGAGATGGATCAACGAGACGTGGTCAGGTCTTGGAGGTTGATGGGGAGAAAGCTGTTGTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT