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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacaccattaatagtaacactctgtttccacacttttttctttgcaacccttattaactatatccctggcctctggcctatctaacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCATGTGACCGAAATGAAGAATTGGCAGCTAACTATCTATTGGAGAACTCAG

Basic information

species Arabidopsis thaliana
transcript AT1G79650.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G23930.1 (Glycine max), 3'ss of exon 12
gtaaaacaccattaatagtaacactctgtttccacacttttttctttgcaacccttattaactatatccctggcctctggcctat--ctaacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCATGTGACCGAAATGAAGAATTGGCAGCTAACTATCTATTGGAGAACTCAG
|||   |||   |  | ||  |      | | |   |  ||  | ||   |   | |||   | |     | |  | |  | |||   |   |||||||||| |||||||||||||||||||  || ||||| || ||  | |||||||||||  ||||  |||||||||| |||||| ||||||||||  | |
gtatgtcactccttcttgt--cgtctaatatacgtgccgttgccattttcattttcatt---tctgctgattgatttttacttattattcgtagCTCGAGGCTATGGGATTTGATAGAGCCTCGGTGATAGAGGCATTTTTGGCATGTGACCGTGATGAGCAATTGGCAGCCAACTATTTATTGGAGAATGCTG

upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 11
gta---aaacaccattaatagtaacactctgtttccacacttttttctttgcaacccttattaactatatccctggcctctggcctatc--taacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCATGTGACCGAAATGAAGAATTGGCAGCTAACTATCTATTGGAGAACTCAG
|||    ||   || |  |  |   | |||  |   | || | |  | |||| |   | |||     |     | |  | |  | |||   |   |||| ||||| |||||||||||||||||||  || |||||||| ||  | |||||||||||  ||||  |||||||||| |||||| ||||||||||  | |
gtatgtcaatgtcactcctttttgtagtctaataatatacgtgt--cattgcgattttcatt---cctgctgattgatttttacttattattcgtagCTTGAGGCTATGGGATTTGATAGAGCCTCGGTGATAGAAGCATTTTTGGCATGTGACCGTGATGAGCAATTGGCAGCCAACTATTTATTGGAGAATGCTG

upper sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0018g01400.t01 (Vitis vinifera), 3'ss of exon 11
gta-aaacaccattaatagtaacactctgtttccacacttttttctttgcaacccttattaactatatccctggcc----tctggcctatctaacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCATGTGACCGAAATGAAGAATTGGCAGCTAACTATCTATTGGAGAACTCAG
||  | || || |      | | |||  ||  |     ||||| ||||  |   | | |||   || | |||   |    ||    |       ||||| ||||||||||||||||| |||||  | || || || || ||| | || ||||| |||||||||||||||||||  |||||||| ||||||||  | |
gtgtagactccttcctccttgatact--gtccctctcttttttgcttttaagttcattttataaattttcctaatcataatcaattcccctccccagCTTGAGGCAATGGGATTTGACAGAGCTCTTGTCATTGAGGCATTCTTAGCTTGTGATCGAAATGAAGAATTGGCAGTCAACTATCTGTTGGAGAATGCTG

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|116469868|gb|EG512460.1|EG512460
EST:     TGCCACATGCCATTAACGTTACCCCAGCAGAACAAGAAGCGATTCAACGG                         CTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCA
genomic: TGCCACATGCCATTAACGTTACCCCAGCAGAACAAGAAGCGATTCAACGGgtaaaacacc ... tatctaacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCA
EST: gi|116469869|gb|EG512461.1|EG512461
EST:     TGCCACATGCCATTAACGTTACCCCAGCAGAACAAGAAGCGATTCAACGG                         CTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCA
genomic: TGCCACATGCCATTAACGTTACCCCAGCAGAACAAGAAGCGATTCAACGGgtaaaacacc ... tatctaacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttctttgcaacccttattaactatatccctggcctctggcctatctaacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCATGTGACCGAAATGAAGAATTGGCAGCTAACTATCTATTGGAGAACTCAG
                  tattaac  putative branch site (score: 1)
                                           cctatct  putative PPT
                 ttattaactatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacaccattaatagtaacactctgtttccacacttttttctttgcaacccttattaactatatccctggcctctggcctatctaacagCTCGAGGCAATGGGATTTGATAGAGCCTTAGTAATAGAAGCGTTCCTCGCATGTGACCGAAATGAAGAATTGGCAGCTAACTATCTATTGGAGAACTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA