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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattaccgttttctttctttcttttttctacatcattacttgttttgtttttacaacttccactgtggtcgtttatccataacataattgaagagactgaaatctgaatccttgcggtcgcttttacatggattttatcccaattcttacacgactttgaatttatcttgtaacagCGTATACCAAACCCTGTTTATCTTTTCCAAGGAATTGTCCTACGCAGAGGTGCCAAAGGAACCGGGATGAAATCCATTGAACTAGCATTGTCCATGTGCG

Basic information

species Arabidopsis thaliana
transcript AT1G08660.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G05340.1 (Glycine max), 3'ss of exon 8
gtatgattaccgttttctttctttcttttttctacatcattacttgttttgtttttacaacttccactg--tggtcgtttatccataacataattgaagagactgaaatctgaatccttgcggtcgcttttacatggattttatcccaattcttacacgactttgaatttatcttgtaacagCGTATACCAAACCCTGTTTATCTTTTCCAAGGAATTGTCCTACGCAGAGGTGCCAAAGGAACCGGGATGAAATCCATTGAACTAGCATTGTCCATGTGCG
                                    | |  |  |||| | |  | || | ||  | ||  || |  ||  |  || |  | | |     |   | || ||| || |||     |  | |   || ||||| ||||  ||||||       ||  | |   | || | ||||  |||||| || || || ||||| |||||||||||||| |||||  |||||||||||||||| || |||||||| |||||  ||||| | |||||||| |
-----------------------------------gtgaaaatctgttctttgataactatttt-attgaatgctttttggtatatgagctcaatacgatgggagcaa-ctggatacttagttactttctagaatagattt-atccgcattctt-------ttgaactaccttttatgacagACTATACCCAATCCAGTCTATCTCTTCCAAGGAATTGTACTACGTCGAGGTGCCAAAGGAACTGGAATGAAATCTATTGAGTTAGCACTCTCCATGTGTG

upper sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G27540.1 (Glycine max), 3'ss of exon 1
gtatgattaccgttttctttctttcttttttctacatcattacttgttttgtttttacaacttccactgtggtcgtttatccataacataattgaagagactgaaatctgaatccttgcggtcgcttttacatggattttatcccaattcttacacgactttgaatttatcttgtaacagCGTATACCAAACCCTGTTTATCTTTTCCAAGGAATTGTCCTACGCAGAGGTGCCAAAGGAACCGGGATGAAATCCATTGAACTAGCATTGTCCATGTGCG
                                                      | | ||  |   || || |   |  |  ||   ||  ||   |  | |   | || ||| |    ||  ||   |  ||  ||  |      | | ||  || || ||         || | ||||  |||||| || || || ||||| |||||||||||||| |||||| | |||||||||||||| || |||||||| |||||  ||||| | |||||||| |
-----------------------------------------------------gtaagaatctgttctttgataactattttattgaatgtttttcggta-tatgagctcaatacagatgggagcaactggatacatagtt-----acttttgaactacctt---------ttatgacagACTATACCCAATCCAGTATATCTCTTCCAAGGAATTGTACTACGCCGTGGTGCCAAAGGAACAGGAATGAAATCTATTGAGTTAGCACTCTCCATGTGTG

upper sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv14s0068g01150.t01 (Vitis vinifera), 3'ss of exon 8
gtatgattaccgttttctttctttcttttttctacatcattacttgttttgtttttacaacttccactgtggtcgtttatccataacataattgaagagactgaaatctgaatccttgcggtcgcttttacatggattttatcccaattcttacacgactttgaatttatcttgtaacagCGTATACCAAACCCTGTTTATCTTTTCCAAGGAATTGTCCTACGCAGAGGTGCCAAAGGAACCGGGATGAAATCCATTGAACTAGCATTGTCCATGTGCG
                                                       | |   || || | || | |  | |  ||  | ||||||||   || | ||||    | |||||  | ||      |||  ||| ||    ||| ||       |||  | |||| |     ||| |||| | ||| || ||||||||||||||||| ||||| || |||||||||||||||||||| || |||||||| || ||||||||| | |||||||| |
-----------------------------------------------------cattctcttttcattctgcttggatttttatgtcttaattgaa---acagtaatcc---ttcttgcaatggc------atgattttgat---gattttt-------ttttcacttattt-----cagAGTATTCAAAATCCAGTTTATCTTTTCCAAGGTATTGTGCTTCGCAGAGGTGCCAAAGGAACTGGAATGAAATCTATAGAACTAGCACTTTCCATGTGTG

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|164225882|gb|ES070150.1|ES070150
EST:     TGCTTATAATAAAAAGTGTGACCCACCGAGACTTCAATGAAATGATAAAG                         CGTATACCAAACCCTGTTTATCT
genomic: TGCTTATAATAAAAAGTGTGACCCACCGAGACTTCAATGAAATGATAAAGgtatgattac ... cttgtaacagCGTATACCAAACCCTGTTTATCT
EST: gi|164100773|gb|ES051386.1|ES051386
EST:     TGCTTATAATAAAAAGTGTGACCCACCGAGACTTCAATGAAATGATAAAG                         CGTATACCAAACCCTGTTTATCT
genomic: TGCTTATAATAAAAAGTGTGACCCACCGAGACTTCAATGAAATGATAAAGgtatgattac ... cttgtaacagCGTATACCAAACCCTGTTTATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttacatggattttatcccaattcttacacgactttgaatttatcttgtaacagCGTATACCAAACCCTGTTTATCTTTTCCAAGGAATTGTCCTACGCAGAGGTGCCAAAGGAACCGGGATGAAATCCATTGAACTAGCATTGTCCATGTGCG
                      ttcttac  putative branch site (score: 2)
                                        tttatctt  putative PPT
                                  tttgaatttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgattaccgttttctttctttcttttttctacatcattacttgttttgtttttacaacttccactgtggtcgtttatccataacataattgaagagactgaaatctgaatccttgcggtcgcttttacatggattttatcccaattcttacacgactttgaatttatcttgtaacagCGTATACCAAACCCTGTTTATCTTTTCCAAGGAATTGTCCTACGCAGAGGTGCCAAAGGAACCGGGATGAAATCCATTGAACTAGCATTGTCCATGTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA