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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttctttctccatactttcgtcatattatctaagcaagctcttcacaagttactatcttcttttggattatttttcagTGTCTTCACTCCATACTATTCCGAGGTTGTGCTATACAGCATGGCTGAACTCACCAAGAGAAATGAGGATGGAATATCAATACTGTTTTATCTTCAGAAA

Basic information

species Arabidopsis thaliana
transcript AT3G07160.1
intron # 30
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 30
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 32
gtatttctttctccatactttcgtcatattatctaagcaagctcttcacaagttactatcttcttttggattatttttcagTGTCTTCACTCCATACTATTCCGAGGTTGTGCTATACAGCATGGCTGAACTCACCAAGAGAAATGAGGATGGAATATCAATACTGTTTTATCTTCAGAAA
|||  ||| |   |    ||     | ||||| ||  |    | ||  || | |  |||||| ||||    | || | |||||| |||||||| || ||||| ||| |||||||||| |||||||||||||||   |||| |||||| ||||| || |||||  |||| || |||||||| 
gtaaatctcttctc----ttggaagaaattat-tacccttagtgttttcatgct--tatcttttttt----ttttgtgcagTGTTTTCACTCCTTATTATTCTGAGATTGTGCTATATAGCATGGCTGAACTCCTAAAGAAAAATGAAGATGGCATTTCAATTTTGTTCTACCTTCAGAAG

upper sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 30
lower sequence: GLYMA10G44150.2 (Glycine max), 3'ss of exon 30
gtatttctttctccatactttcgtcatattatctaagcaagctcttcacaagttactatcttcttttggattatttttcagTGTCTTCACTCCATACTATTCCGAGGTTGTGCTATACAGCATGGCTGAACTCACCAAGAGAAATGAGGATGGAATATCAATACTGTTTTATCTTCAGAAA
|||  |||||   | |          ||||| || ||     | ||||        |||| | |||||  |   | | |||||| |||||||| || ||||| ||| ||||||| || |||||||||||||||   |||| ||| || || || || |||||  |||| || |||||||| 
gtaaatcttttctcttgaaagaaat-tattaccttagtg---ttttcatgc----ttatccttttttgtgtg--tgtgcagTGTTTTCACTCCTTATTATTCTGAGATTGTGCTTTATAGCATGGCTGAACTCCTAAAGAAAAACGAAGACGGCATTTCAATTTTGTTCTACCTTCAGAAG

upper sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 30
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 27
---------------gtatttctttctccatactttcgtcatatt---atctaagcaagctcttcacaagttactatcttcttt-tggattatttttcagTGTCTTCACTCCATACTATTCCGAGGTTGTGCTATACAGCATGGCTGAACTCACCAAGAGAAATGAGGATGGAATATCAATACTGTTTTATCTTCAGAAA
                 |||   || ||     |||  | |||||   | ||||||         | |   | ||   |||||| |   ||  | | |||||| ||||||||||| ||||| |||  |||||| || || |||| |||||||   |||| |||||||||||||||||||| | ||||||| || ||||||
gtagtataattctctcgattcaattttcttgtatttaatgatattgatacctaagcttataaaatatagcatcctcagttctttctatgtttctgtacagTGTGTTCACTCCATATTATTCTGAGACTGTGCTTTATAGTATGGATGAACTCCAAAAGAAAAATGAGGATGGAATATCAACATTGTTTTACCTCCAGAAA

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|164153578|gb|ES045653.1|ES045653
EST:     TGTGCCACCACCTAAGTCTGTCCGCAAGATGTTATCCTTCAG                         TGTCTTCACTCCATACTATTCCGAGG
genomic: TGTGCCACCACCTAAGTCTGTCCGCAAGATGTTATCCTTCAGgtatttcttt ... tatttttcagTGTCTTCACTCCATACTATTCCGAGG
EST: gi|116421625|gb|EG464217.1|EG464217
EST:     TTCATGGATGTGCCACCACCTAAGTCTGTCCGCAAGATGTTATCCTTCAG                         TGTCTTCACTCCATACTATTCCGAGGTTGTGCTATACAGCATGGCTGAACT
genomic: TTCATGGATGTGCCACCACCTAAGTCTGTCCGCAAGATGTTATCCTTCAGgtatttcttt ... tatttttcagTGTCTTCACTCCATACTATTCCGAGGTTGTGCTATACAGCATGGCTGAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatctaagcaagctcttcacaagttactatcttcttttggattatttttcagTGTCTTCACTCCATACTATTCCGAGGTTGTGCTATACAGCATGGCTGAACTCACCAAGAGAAATGAGGATGGAATATCAATACTGTTTTATCTTCAGAAA
                                            ttatttttc  CT-rich tract
                                     ttttggattattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttctttctccatactttcgtcatattatctaagcaagctcttcacaagttactatcttcttttggattatttttcagTGTCTTCACTCCATACTATTCCGAGGTTGTGCTATACAGCATGGCTGAACTCACCAAGAGAAATGAGGATGGAATATCAATACTGTTTTATCTTCAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA