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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtatattctttagtgtgattcagattgatattgagaagtgatgaacaaatcctgtgttttattgtactgaatggaataattgctggctgatttgaatagGCATCGTTGAAGACAGAGAGGGAGAAGAAGAAAGAAATGTACTTTCCAATAAGGAAGTATGCTATTAAGGTGTAAGCTTTTATCTTGATCACATCAATTT

Basic information

species Arabidopsis thaliana
transcript AT2G39390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G39390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G38480.1 (Glycine max), 3'ss of exon 3
gta-tttgtatatt-ctttagtgtgattcagattgatattgagaagtgatgaacaaatcctgtgttttattgtactgaatggaataattgctggctgatttgaatagGCATCGTTGAAGACAGAGAGGGAGAAGAAGAAAGAAATGTACTTTCCAATAAGGAAGTATGCTATTAAGGTGTAAGCTTTTATCTTGATCACATCAATTT--
||| ||| ||| || |  | ||  |||     ||  | ||  | | |  ||      | || | |||  |  |  | |        ||| || | |  |      ||||||| |||||||||||||||||||||||||||||  | || || ||| ||||||| |||||||| |||||||||   ||||     |||  |||  ||   
gtaatttatatgttacggttgtaggatgtgccttattcttttgtaat--tgtcttgcttctatatttgttgctcataagcttttgcatttcttgttattc-----agGCATCATTGAAGACAGAGAGGGAGAAGAAGAAAGAGTTATATTTCCCACTAAGGAAATATGCTATCAAGGTGTAA--CTTTAGAGCAATCTTATCGGTTAAT

upper sequence: AT2G39390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G43770.2 (Glycine max), 3'ss of exon 2
gtatttgtatattctttagtgtgattcagattgatattgagaagtgatgaacaaatcctgtgttttattgtactgaatggaataattgctggctgatttgaatagGCATCGTTGAAGACAGAGAGGGAGAAGAAGAAAGAAATGTACTTTCCAATAAGGAAGTATGCTATTAAGGTGTAAGCTTTTATCTTGATCACATCAATTT--
  ||||  ||     | | |||        ||  | ||  | | |  ||      || ||   ||| |||  |   |||  ||  ||  |  ||  ||     ||||||| |||||||||||||||||||||||||||||  | || || ||| | ||||| |||||||| |||||||||   ||||     |||  |||  ||   
ccatttagattggtatgattgtaggatgccttattcttttgtaat--tgttttgctcatgatatttgttgctc---atgagatttttcatttcttgttcatgcagGCATCATTGAAGACAGAGAGGGAGAAGAAGAAAGAGTTATATTTCCCACTGAGGAAATATGCTATCAAGGTGTAA--CTTTAGAGCAATCTTATCTGTTAAT

upper sequence: AT2G39390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0317g00130.t01 (Vitis vinifera), 3'ss of exon 3
gtatttgtatattctttagtgtgattcagattgatattgagaagtgatgaacaaatcctgtgttttattg-tactgaatggaataattgctggctgatttgaatagGCATCGTTGAAGACAGAGAGGGAGAAGAAGAAAGAAATGTACTTTCCAATAAGGAAGTATGCTATTAAGGTGTAAGCTTTTATCTTGATCACATCAATTT--
   ||  | |   ||| ||  |  | ||   |  ||    |     |     |  |  |||  ||  ||| || | | |    | | |  |  ||  ||     |||  || || |||||||| ||||| |||||||  || |||||||| || || ||||||||||||||||||||||| |     |||   || |  |   |    
--gttactgtgc-cttcagaattttccatgcttgtagcccgtttctagctttatgtattgttattccttggtattaagtct--tcactattttcttgttcct-cagGTGTCATTAAAGACAGAAAGGGAAAAGAAGAGGGAGATGTACTTCCCCATGAGGAAGTATGCTATTAAGGTGTAGGTCAGGATC--AATTATGTTTGTCATT

upper sequence: AT2G39390.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0004g04020.t01 (Vitis vinifera), 3'ss of exon 4
gtatttgtatattctttagtgtgattcagattgatattgagaagtgatgaacaaatcctgtgttttattgtactgaatggaataattgctggctgatttgaatagGCATCGTTGAAGACAGAGAGGGAGAAGAAGAAAGAAATGTACTTTCCAATAAGGAAGTATGCTATTAAGGTGTAAGCTTTTATCTTGATCAC-ATCAATTT
   ||  |    ||     |||| |           || |    || || ||| ||   |  | ||     |||||   |  || || |||  | |  |    ||||||| |||||||| ||  | ||||| ||||| || ||||| | ||| || ||||||||||| |||||||||||||| |  || |  |     ||  |   
---ttcattccatcacacttgtgttaagtgccttgcttaattcatgttgtacacatgg-gcatctttaaaaactgatctgcttatttcctg-ttcaaatatgcagGCATCTTTGAAGACTGAACGAGAGAAAAAGAAGGAGATGTATTATCCCATGAGGAAGTATGCCATTAAGGTGTAAGCGTGGATTTACACAGTTATGGACG-

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|86076065|gb|DR371822.1|DR371822
EST:     TTCGTCCCAAGAAGACTAGAGCCATCAGGAGGAGACTCACTAAGCATCAG                         GCATCGTTGAAGACAGAGAGGGAGAAGAAGAAAGAAATGTACTTTCCAATA
genomic: TTCGTCCCAAGAAGACTAGAGCCATCAGGAGGAGACTCACTAAGCATCAGgtatttgtat ... atttgaatagGCATCGTTGAAGACAGAGAGGGAGAAGAAGAAAGAAATGTACTTTCCAATA
EST: gi|124737313|gb|EH828715.1|EH828715
EST:     TTCGTCCCAAGAAGACTAGAGCCATCAGGAGGAGACTCACTAAGCATCAG                         GCATCGTTGAAGA
genomic: TTCGTCCCAAGAAGACTAGAGCCATCAGGAGGAGACTCACTAAGCATCAGgtatttgtat ... atttgaatagGCATCGTTGAAGA
EST: gi|125022580|gb|EL094849.1|EL094849
EST:     TTCGTCCCAAGAAGACTAGAGCCATCAGGAGGAGACTCACTAAGCATCAG                         GCATCGTTGAAGA
genomic: TTCGTCCCAAGAAGACTAGAGCCATCAGGAGGAGACTCACTAAGCATCAGgtatttgtat ... atttgaatagGCATCGTTGAAGA
EST: gi|152038390|gb|AV821605.2|AV821605
EST:     TTCGTCCCAAGAAGACTAGAGCCATCAGGAGGAGACTCACTAAGCATCAG                         GCATCGTTGAAGACAGAGAGGGAGAAGAAGAAAGAAATGTACTTTCCAATA
genomic: TTCGTCCCAAGAAGACTAGAGCCATCAGGAGGAGACTCACTAAGCATCAGgtatttgtat ... atttgaatagGCATCGTTGAAGACAGAGAGGGAGAAGAAGAAAGAAATGTACTTTCCAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaatcctgtgttttattgtactgaatggaataattgctggctgatttgaatagGCATCGTTGAAGACAGAGAGGGAGAAGAAGAAAGAAATGTACTTTCCAATAAGGAAGTATGCTATTAAGGTGTAAGCTTTTATCTTGATCACATCAATTT
                                        ggctgat  putative branch site (score: 4)
            ttttattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgtatattctttagtgtgattcagattgatattgagaagtgatgaacaaatcctgtgttttattgtactgaatggaataattgctggctgatttgaatagGCATCGTTGAAGACAGAGAGGGAGAAGAAGAAAGAAATGTACTTTCCAATAAGGAAGTATGCTATTAAGGTGTAAGCTTTTATCTTGATCACATCAATTT

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