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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGATACTTTGTCATTCCATTGTGGAGAGGAAATGGTTACATAACAATGTTTGCTCAAGgttctaactttaatcctccattatatatacatctttcatttccttgtgagaaatttatatgaaatggttacataacaatgcttgctccagatttgtggta...

Basic information

species Arabidopsis thaliana
transcript AT2G34050.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G34050.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G12960.1 (Glycine max), 5'ss of exon 3
CCGATACTTTGTCATTCCATTGTGGAGAGGAAATGGTTACATAACAATGTTTGCTCAAGgttctaactttaatc-ctccattatatatacatctt---tcatttccttgtgagaaatttatatgaaatggttacataacaatgcttgctccagatttgtggta-
|||||| ||||||||||| || ||||| |||| ||| ||||  |||||||||| |||||||| | ||   |||| |||  |||| |||   |      ||| |   |  |  ||  |||| || |||    |   | |||   ||   | |  ||||||  |  
CCGATATTTTGTCATTCCTTTATGGAGGGGAAGTGGATACACGACAATGTTTGTTCAAGgtt-tgacaaaaatcactctcttatttatgtgtaaaaaatcaataattgttttgacttttaaatcaaa--actgtgttacac--ctgattgctaatttgtatttg

upper sequence: AT2G34050.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv10s0003g00660.t01 (Vitis vinifera), 5'ss of exon 3
CCGATACTTTGTCATTCCATTGTGGAGAGGAAATGGTTACATAACAATGTTTGCTCAAGgttctaactttaatcctccattatatatacatctttcatttccttgtgagaaatttatatgaaatggttacataacaatgcttgctccagatttgtggta-------
|||  | ||||||||||| ||||||||||||| ||||||   ||||||||| ||||||||||| | || ||||       | | |  | || ||   |     | | | |   |||    |   |  |  ||   ||  |||| |    |||||||| |       
CCGGCATTTTGTCATTCCTTTGTGGAGAGGAAGTGGTTATGCAACAATGTTCGCTCAAGgttcgatctctaattaatagcttttttcatattttatgtagtgattttatactgtta----aggggcctgtatgggaa-acttgattt--atttgtggcaaggaaag
















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|301501274|gb|HO206814.1|HO206814
EST:     TGTCATTCCATTGTGGAGAGGAAATGGTTACATAACAATGTTTGCTCAAG                         TTGAAGCGCCTCACATGATTTTTACTGGTCTCGAAGACTACAAAGCAAGAG
genomic: TGTCATTCCATTGTGGAGAGGAAATGGTTACATAACAATGTTTGCTCAAGgttctaactt ... attgtggcagTTGAAGCGCCTCACATGATTTTTACTGGTCTCGAAGACTACAAAGCAAGAG
EST: gi|86077967|gb|DR373724.1|DR373724
EST:     TGTCATTCCATCGTGGAGAGGAAATGGTTACATAACAATGTTTGCTCAAG                         TTGAAGCGCCTCACATGATTTTTACTGGTCTCGAAGACTACAAAGCAAGAG
genomic: TGTCATTCCATTGTGGAGAGGAAATGGTTACATAACAATGTTTGCTCAAGgttctaactt ... attgtggcagTTGAAGCGCCTCACATGATTTTTACTGGTCTCGAAGACTACAAAGCAAGAG
EST: gi|124861111|gb|EH945548.1|EH945548
EST:     TGTCATTCCATTGTGGAGAGGAAATGGTTACATAACAATGTTTGCTCAAG                         TTGAAGCGCCT
genomic: TGTCATTCCATTGTGGAGAGGAAATGGTTACATAACAATGTTTGCTCAAGgttctaactt ... attgtggcagTTGAAGCGCCT
EST: gi|164210134|gb|ES170216.1|ES170216
EST:     GAGAGGAAATGGTTACATTACAATGTTTGCTCAAG                         TTGAAGCGCCTCACATGATTTTTACTGGTCTCGAAGACTACAAAGCAAGAG
genomic: GAGAGGAAATGGTTACATAACAATGTTTGCTCAAGgttctaactt ... attgtggcagTTGAAGCGCCTCACATGATTTTTACTGGTCTCGAAGACTACAAAGCAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGATACTTTGTCATTCCATTGTGGAGAGGAAATGGTTACATAACAATGTTTGCTCAAGgttctaactttaatcctccattatatatacatctttcatttccttgtgagaaatttatatgaaatggttacataacaatgcttgctccagatttgtggta

- - - - - - - - - -  GTGGAG
- - - - - - - - - - - TGGAGA
- - - - - - - - - - - - GAGAGG
- - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgctc