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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatatttagtcttgatttctgatttcttcccatttttctgtttcttttctgagatcactacaagattgttgttgtgaattgttgttgtgatggttgaaaagatctgagatttactgctgtatagatgttttgtaagagtattggtttgtttgcctggtttttgatttcagCATGCCCGGTATGTTACCTTCCAGTAGAAGAAGCAGTTGCCTTGATGCCAAATGCCCCATCATTTTCCCCTGTTCTTAAGAACTTAACGTATATATATGA

Basic information

species Arabidopsis thaliana
transcript AT1G28240.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G08090.1 (Glycine max), 3'ss of exon 2
gtaagatatttagtcttgatttctgatttcttcccatttttctgtttcttttctgagatcactacaagattgttgttgt--gaattgttgttgtgatggttgaaaagatctgag-atttactgctgtatagatgttttgtaagagtattggtttgtttgcctggtttttgatttcagCATGCCCGGTATGTTACCTTCCAGTAGAAGAAGCAGTTGCCTTGATGCCAAATGCCCCATCATTTTCCCCTGTTCTTAAGAACTTAACGTATATATATGA
||||||| ||  || ||  | | |  ||||| |  || | |   ||| ||   | |  | |  |  |  ||  |   |   | ||  ||  || |    | |||   || |||  ||||   | |   |||   |  ||  |   |  ||     |||| || |||| || ||||||||||||||||||||||||||||  | || |||||  ||||  |  |||||||    || |||  ||| || || |||||||||||||| | ||| |||||
gtaagatctt--gttttactatattgtttctgcaaatatct---tttgttaggtaattttatgaggatgtttcttgagctaggataatttatgaggatatagaaggcatatgaatattttaggttacttagtgttagtggtatgatcctgaacattttggcttgtttgtg-tttcagCATGCCCGGTATGTTACCTTCCCATGGATGAAGCCATTGCACTTGTGCCAAAGTTTCCGTCACCTTCTCCAGTACTTAAGAACTTAACATTTATCTATGA

upper sequence: AT1G28240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0265g00120.t01 (Vitis vinifera), 3'ss of exon 2
gtaagatat--ttagtcttgatttctgatttcttcc-catttttctgtttcttttctgaga-tcacta-caagattgttgttgtgaattgttgttgtgatggttgaaaagatctgagatttactgctgtata--gatgttttgtaagagtattggtttgtttgcctggtttttgatttcagCATGCCCGGTATGTTACCTTCCAGTAGAAGAAGCAGTTGCCTTGATGCCAAATGCCCCATCATTTTCCCCTGTTCTTAAGAACTTAACGTATATATATGA
||||| | |  ||  |   | ||| ||  || |     ||  |  |||    || ||     |||| | || |  | | |||   |  ||   |     | || |    |  || |||  || |  | ||||   ||   |  | | | |  ||  ||  |||| |    ||   |||||||||| || |||||||||||||| || ||||||||  | ||||| ||||||||   |||||||  ||| ||  | ||||| || ||||| | | | |||||
gtaagttttagttgttaaagctttttgggttttaaaatataataatgtgctgttgctatctctcacaaacatgtatttagttccaagatggcatctatgttgtagtttcgtcctaagacatatttatttatatcaatagatcttcaaattgctgagtt-cttgctt--ccttatgtttcagCATGTCCAGTATGTTACCTTCCTGTGGAAGAAGCCATCGCCTTAATGCCAAAATACCCATCACCTTCTCCCTTACTTAATAATTTAACATTTGTCTATGA
















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|164177265|gb|ES042059.1|ES042059
EST:     TTTCACTTTACCTCCCCCACCAGCAGACAGGAAAAGAACAGGACCACGCC                         CATGCCCGGTATGTTACCTTCCAGTAGAAGAAGCAGTTGCCTTGAT
genomic: TTTCACTTTACCTCCCCCACCAGCAGACAGGAAAAGAACAGGACCACGCCgtaagatatt ... ttgatttcagCATGCCCGGTATGTTACCTTCCAGTAGAAGAAGCAGTTGCCTTGAT
EST: gi|163992442|gb|ES117673.1|ES117673
EST:     TTCACTTTACCTCCCCCCACCAGCAGACAGGAAAAGAACAGGACCACGCC                         CATGCCCGGTATGTTACCTTCCAGTAGAAGAAGCAGTTGCCTTGAT
genomic: TTCACTTTACCT-CCCCCACCAGCAGACAGGAAAAGAACAGGACCACGCCgtaagatatt ... ttgatttcagCATGCCCGGTATGTTACCTTCCAGTAGAAGAAGCAGTTGCCTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgtatagatgttttgtaagagtattggtttgtttgcctggtttttgatttcagCATGCCCGGTATGTTACCTTCCAGTAGAAGAAGCAGTTGCCTTGATGCCAAATGCCCCATCATTTTCCCCTGTTCTTAAGAACTTAACGTATATATATGA
                                           ttttgat  putative branch site (score: 4)
                                          ttttt  CT-rich tract
                                          tttttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatatttagtcttgatttctgatttcttcccatttttctgtttcttttctgagatcactacaagattgttgttgtgaattgttgttgtgatggttgaaaagatctgagatttactgctgtatagatgttttgtaagagtattggtttgtttgcctggtttttgatttcagCATGCCCGGTATGTTACCTTCCAGTAGAAGAAGCAGTTGCCTTGATGCCAAATGCCCCATCATTTTCCCCTGTTCTTAAGAACTTAACGTATATATATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC