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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtaacttctgtttcccacaaatctaagtcgcctctaaatatcagcttatagtctcttgtgttccacagGTCTATGTATGGAGCAAACAAAATCCTTATATTCACATGAGTTTCCTTGGTCTGTTCACCTTCACAGCAGCTTACCTACCATGG

Basic information

species Arabidopsis thaliana
transcript AT4G04860.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G11350.3 (Glycine max), 3'ss of exon 3
--------------------gttggtaacttctgtttcccacaaatctaagtcgcctctaaatatcagc-----ttatagtct---cttgtgttccacagGTCTATGTATGGAGCAAACAAAATCCTTATATTCACATGAGTTTCCTTGGTCTGTTCACCTTCACAGCAGCTTACCTACCATGG----------------
                    |    ||| ||   |       | || |   |    || ||  ||   |     ||| ||  |    ||   ||   ||||| || || ||||||||||||||||| |  ||||||||||| ||||| ||||| || || ||||| || || ||||| ||||||                
ccacttatatattttattttggccttaattttaatcgatgtgagatttggattttttccaataattcacgaacattaaagcttaatttttcatttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGGTGCGTAAGCTCTATA

upper sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G27600.1 (Glycine max), 3'ss of exon 3
---------gttggtaacttctgtttccca----caaatctaagtcgcctc-taaatatcagcttatagtctcttgtgttccacagGTCTATGTATGGAGCAAACAAAATCCTTATATTCACATGAGTTTCCTTGGTCTGTTCACCTTCACAGCAGCTTACCTACCATGG
          ||  ||  ||    | | |     |||||||    |   ||  |||  | |     || | | |  | || ||  ||| || || ||||||||||||||||| |  ||||||||||| ||||| ||||| || || ||||| || || ||||| ||||||
gtaagtcacatttttatttttcactcctcgtgttcaaatctgtcacaattcacaaacgtgaaagcttaatttttcttttttca--gGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG

upper sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G11350.2 (Glycine max), 3'ss of exon 3
--------------------gttggtaacttctgtttcccacaaatctaagtcgcctctaaatatcagc-----ttatagtct---cttgtgttccacagGTCTATGTATGGAGCAAACAAAATCCTTATATTCACATGAGTTTCCTTGGTCTGTTCACCTTCACAGCAGCTTACCTACCATGG
                    |    ||| ||   |       | || |   |    || ||  ||   |     ||| ||  |    ||   ||   ||||| || || ||||||||||||||||| |  ||||||||||| ||||| ||||| || || ||||| || || ||||| ||||||
ccacttatatattttattttggccttaattttaatcgatgtgagatttggattttttccaataattcacgaacattaaagcttaatttttcatttttcagGTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG

upper sequence: AT4G04860.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0116g00010.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------gttggtaactt-ctgtttcccacaaatctaagtcgcct---ctaaatatcagcttata--gtctcttgtgttccacagGTCTATGTATGGAGCAAACAAAATCCTTATATTCACATGAGTTTCCTTGGTCTGTTCACCTTCACAGCAGCTTACCTACCATGG
                             |  | |   ||  || || |    | | |    |  ||    |  || ||   |||    || | |  ||||  |||||| ||||| |||||||| |||||||||| ||| || ||||||||| | || || || ||||||||||| || ||||| ||||||
gttagttaatttttctttgctcacacatagaagatgttttattggttacagtcattgtgcaacaactgttttggatgtcttgttactctgtttttcctgttgtacagGTTTATGTGTGGAGCAAGCAAAATCCTTTTATCCATATGAGTTTCTTGGGCCTCTTTACCTTCACAGCGGCCTACCTTCCATGG

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|125306944|gb|EL321029.1|EL321029
EST:     CTTTCATGATG                         GTCTATGTATGGAGCAAACAAAATCCTCATATTCACATGAGTTTCCTTGGT
genomic: CTTTCATGATGgttggtaact ... tgttccacagGTCTATGTATGGAGCAAACAAAATCCTTATATTCACATGAGTTTCCTTGGT
EST: gi|124715747|gb|EH807149.1|EH807149
EST:     TTTGCTAAAATCATCTTCCTCAGCAACTCATTAACTTTCATGATG                         GTCTATGTATGGAGCAAAACAAAATCCTTATATTCACATGAGTTTCCTT
genomic: TTTGCTAAAATCATCTTCCTCAGCAACTCATTAACTTTCATGATGgttggtaact ... tgttccacagGTCTATGTATGGAGCAAA-CAAAATCCTTATATTCACATGAGTTTCCTT
EST: gi|164173188|gb|ES168557.1|ES168557
EST:     CATCATTTGCTAAAATCATCTTCCTCAGCAACTCATTAACTTTCATGATG                         GTCTATGTATGGAGCAAACAAAATCCTT
genomic: CATCATTTGCTAAAATCATCTTCCTCAGCAACTCATTAACTTTCATGATGgttggtaact ... tgttccacagGTCTATGTATGGAGCAAACAAAATCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccacaaatctaagtcgcctctaaatatcagcttatagtctcttgtgttccacagGTCTATGTATGGAGCAAACAAAATCCTTATATTCACATGAGTTTCCTTGGTCTGTTCACCTTCACAGCAGCTTACCTACCATGG
                  ctctaaa  putative branch site (score: 3)
                                      tctcttgt  putative PPT
                   tctaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtaacttctgtttcccacaaatctaagtcgcctctaaatatcagcttatagtctcttgtgttccacagGTCTATGTATGGAGCAAACAAAATCCTTATATTCACATGAGTTTCCTTGGTCTGTTCACCTTCACAGCAGCTTACCTACCATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT