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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttaacaacctcatgcttctgacaggagatcgttcattacttttgcctgtattgatttgctgataattgttgatccattcatctttgtttaagCTGCTGGAGCATGTAACATTTGTCGACACCCCTGGAGTTTTATCAGGGGAAAAACAAAGAACACAGCGAGCATATGATTTCACTGGTGTTACATCATGGT

Basic information

species Arabidopsis thaliana
transcript AT3G20290.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 11
gtatgtttaacaacctcatgcttctgacaggagatcgttcattacttttgcctgtattgattt-gctgataattgttgatccattcatctttgtttaagCTGCTGGAGCATGTAACATTTGTCGACACCCCTGGAGTTTTATCAGGGGAAAAACAAAGAACACAGCGAGCATATGATTTCACTGGTGTTACATCATGGT
|||| ||       ||    ||  | |    |  || |   || | ||    || | | |    |  | ||||||||      ||   | |||   ||||| ||||| ||| |||| ||||| ||||| ||||||||||||||||||||||| ||  ||||||||||    ||||| |||||||| |||||||||||||
gtatattccttc-tcttgcactgattattctacttcatatttttcattatgttgcactcagaaagaagctaattgttagcatcttttacattgcc-aagCTACTGGATCATATAACCTTTGTGGACACTCCTGGAGTTTTATCAGGGGAAAAGCAGCGAACACAGCGTAGCTATGACTTCACTGGAGTTACATCATGGT

upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 11
gtatgtttaacaacctcatgcttctgacaggagatcgttcattacttttgcctgtattgatttgctgataattgttgatccattcatctttgtttaa-gCTGCTGGAGCATGTAACATTTGTCGACACCCCTGGAGTTTTATCAGGGGAAAAACAAAGAACACAGCGAGCATATGATTTCACTGGTGTTACATCATGGT
||| | ||  | |   ||   |    ||   |  |     ||  || ||  ||||     || |    ||  | ||  |  |||     || |  || |||  |||||||  | |||||||| |||| ||||||||||||||| || ||||| |||||||||||  ||  ||||||||| || ||||| ||||| ||||
gtaagcttttctataccaaatta--aaccaaaattaagatatatctctt--ctgtggcatttggaacttacctatttttttattatcaattatccaaagCTATTGGAGCACATTACATTTGTTGACAGCCCTGGAGTTTTATCTGGAGAAAAGCAAAGAACACATAGACAATATGATTTTACAGGTGTAACATCTTGGT

upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA02G46350.2 (Glycine max), 3'ss of exon 11
gtatgtttaacaacctcatgcttctgacaggagatcgttcattacttttgcctgtattgatttgctgataattgttgatccattcatctttgtttaa-gCTGCTGGAGCATGTAACATTTGTCGACACCCCTGGAGTTTTATCAGGGGAAAAACAAAGAACACAGCGAGCATATGATTTCACTGGTGTTACATCATGGT
||| ||| | |       |   ||||     | |  ||| |  |  ||| ||| ||| |      | | |||||   |  | ||     ||||  || ||| ||||| ||  | |||||||| ||||| || |||||| |||| || ||||| ||| | ||||| |||||||||||||| || ||||| ||||| ||||
gtaagttgatc-------tagatctgttcaaaaa--gtttacaagatttccctttatag---catttagaattg---actctttttcaattgtccaaagCTACTGGAACACATCACATTTGTTGACACTCCGGGAGTTCTATCTGGAGAAAAGCAACGCACACAACGAGCATATGATTTTACGGGTGTAACATCTTGGT

upper sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 11
gtatgtttaacaacctcatgcttctgacaggagatcgttcattacttttgcctgtattgatttgctgataattgttgatccattcatctttgtttaagCTGCTGGAGCATGTAACATTTGTCGACACCCCTGGAGTTTTATCAGGGGAAAAACAAAGAACACAGCGAGCATATGATTTCACTGGTGTTACATCATGGT
   ||  | |  ||   ||  || | |  | |  |  |  ||||   ||  |||||     |      ||||  || ||    |||         ||||| ||||||||  | || ||||| || || ||||||||| ||||||| ||||| ||| ||||||||||||| || ||||| |||||||| ||||||||||
--gtgagttattactctataattatcatggaaatttctagattatcatt--ctgtagcacctgaaacttaatcttttatatgatca---------aagCTACTGGAGCACATCACGTTTGTGGATACTCCTGGAGTTCTATCAGGAGAAAAGCAACGAACACAGCGAGCCTACGATTTTACTGGTGTAACATCATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttgcctgtattgatttgctgataattgttgatccattcatctttgtttaagCTGCTGGAGCATGTAACATTTGTCGACACCCCTGGAGTTTTATCAGGGGAAAAACAAAGAACACAGCGAGCATATGATTTCACTGGTGTTACATCATGGT
                                       ttcatcttt  CT-rich tract
           tattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttaacaacctcatgcttctgacaggagatcgttcattacttttgcctgtattgatttgctgataattgttgatccattcatctttgtttaagCTGCTGGAGCATGTAACATTTGTCGACACCCCTGGAGTTTTATCAGGGGAAAAACAAAGAACACAGCGAGCATATGATTTCACTGGTGTTACATCATGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC