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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatttaccactaccctctgcttcttgtgtaattcctttgggagctttgttatatctcatgaactctccttgttaagtctccatctgtatgtggtctcctccatttgcagCCTGCTCATGAGAAGATTGGTGTGGTAGATTCACAGTGGATTATCCATCAAGTGATTCCTTCCCTTGGAAGTCAG

Basic information

species Arabidopsis thaliana
transcript AT1G08040.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 12
gttatttaccactaccctctgcttcttgtgtaattcctttgggagctttgttatatctc-atgaactctccttgttaagtctccatctgtatg--tggtctcctcca--tttgcagCCTGCTCATGAGAAGATTGGTGTGGTAGATTCACAGTGGATTATCCATCAAGTGATTCCTTCCCTTGGAAGTCAG
                                      |  | |||     ||  | || | |   | | |   |    | ||||||||| ||  || |    |  |  |||||||||||| |||||||| || ||||| || ||||| || |||||| | ||||||||| ||||||| ||||| |  |||
-------------------------------------gtatgcagcacacatacttgtctacggcttttgcccatatcatttccatctgtctggctgattattttaatctttgcagCCTGCACATGAGAAAATCGGTGTCGTTGATTCCCAATGGATTGTACATCAAGTGGTTCCTTCTCTTGGGAACCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 12
gttatttaccactaccctctgcttcttgtgtaattcctttgggagctttgttatatctcatgaactctccttgttaagtctccatctgtatgtggtctcctccatttgcagCCTGCTCATGAGAAGATTGGTGTGGTAGATTCACAGTGGATTATCCATCAAGTGATTCCTTCCCTTGGAAGTCAG
                    |  |    |    ||    ||  |  |||       ||  |  |   || || | ||    |   |   |||     |  | ||||| ||||||||||| || |||||||| || || ||||||||||||||| | || |||||| |||| || || || |  |||
--------------------gtataggttaccttttggctgttaaatttcaccggcctggtagaacttcattatgaatatgctcaccaaatgc---tttgtgcattt-cagCCTGCTCACGAAAAGATTGGGGTTGTTGATTCACAGTGGATTGTTCACCAAGTGGTTCCATCTCTCGGGAACCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 12
gttatttaccactaccctctgcttcttgtgtaattcctttgggagctttgttatatctcatgaactctccttgttaagtctccatctgtatgtggtctcctccatttgcagCCTGCTCATGAGAAGATTGGTGTGGTAGATTCACAGTGGATTATCCATCAAGTGATTCCTTCCCTTGGAAGTCAG
                          | || | ||  |||| |||  |  ||||| |     | |   |  ||||  || ||    ||  | ||   |    |     |||||||||||||| |||||||| || || ||||| ||||||||  | || |||||| ||||||| || || |  |||
-------------------------gtatgca-ttgttttgagagagtc-ttataccattctagcgaac--tgtt--gtttctgaatgcttttgacgttgctcgc---cagCCTGCTCATGAAAAGATTGGAGTTGTCGATTCGCAGTGGATCGTTCACCAAGTGGTTCCTTCTCTGGGGAACCAG

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 12
gttatttaccactaccctctgcttcttgtgtaattcctttgggagctttgttatatctcatgaactctccttgttaagtctccatctgtatgtggtctc-ctccatttgcagCCTGCTCATGAGAAGATTGGTGTGGTAGATTCACAGTGGATTATCCATCAAGTGATTCCTTCCCTTGGAAGTCAG
        |   ||   | |  || |  | |        |   | | || ||||     ||  ||| ||  | | |  ||  |   |   |||        |   ||| |||||||| |||||||| || |||||||| ||||||||||||||||| ||| ||||  | ||||| ||||| || || 
--------cagatattttatatttttcttttgggc----taacaacctttttatcagcaatctactttctatttgacatcaactcataattgttactggattttctttacagCCTGCACATGAGAAAATCGGTGTGGTTGATTCACAGTGGATTATTCATAAAGTAGTACCTTCTCTTGGGAGCCAA

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|86085178|gb|DR380937.1|DR380937
EST:     ATCTTGTTCATGGATGGGGTCTCGATTTTGCTCTCAGACGATGCGTTGAG                         CCTGCTCATGAGAAGATTGGTGTGGTAGATTCACAGTGGATTATCCATCAA
genomic: ATCTTGTTCATGGATGGGGTCTCGATTTTGCTCTCAGACGATGCGTTGAGgttatttacc ... ccatttgcagCCTGCTCATGAGAAGATTGGTGTGGTAGATTCACAGTGGATTATCCATCAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatgaactctccttgttaagtctccatctgtatgtggtctcctccatttgcagCCTGCTCATGAGAAGATTGGTGTGGTAGATTCACAGTGGATTATCCATCAAGTGATTCCTTCCCTTGGAAGTCAG
                                       tctcctccatttgc  CT-rich tract
              ttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatttaccactaccctctgcttcttgtgtaattcctttgggagctttgttatatctcatgaactctccttgttaagtctccatctgtatgtggtctcctccatttgcagCCTGCTCATGAGAAGATTGGTGTGGTAGATTCACAGTGGATTATCCATCAAGTGATTCCTTCCCTTGGAAGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG