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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagagatcttgtcttgaaatcagatggtatgaagtgttgtgaattctcgtgtcttctgaaagaccttagaatatgatgtttcgtttttaactttcccagCTCGCAGAAGCCGCAAAGTCCCAGTTTTCACGTGATCACAGTGATCATCTTGCACTTGTTCGGGCATATGAGGGGTGGAAAAAAGCTGAGGAAGAGTCTG

Basic information

species Arabidopsis thaliana
transcript AT2G01130.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G01130.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 14
-aaagagatcttgt-cttgaaatcagatggtatgaagtgttgtgaattct---cgtgtcttctgaaagaccttagaatatgatgtttcgtttttaactttcccagCTCGCAGAAGCCGCAAAGTCCCAGTTTTCACGT---GATCACAGTGATCATCTTGCACTTGTTCGGGCATATGAGGGGTGGAAAAAAGCTGAGGAAGAGTCTG
  |||   ||  ||  |||  |   || |   |   || || | | || |    ||  |||||    |    |  || |||||| |   || |  |      ||||| |||||  | || ||||  ||||||||| |    ||  ||||||||||||||||||||||||| |||||||| || ||||   | |||||   |||     
tcaaggcgtcaagtgtttgtgactggaggtagtattgttttctaagtttttggtgtaccttctttttggtactgtaa-atgatgctagtttgtccatg----cagCTTGCAGAGTCAGCTAAGTTGCAGTTTTCATGCCGGGACTACAGTGATCATCTTGCACTTGTTCGTGCATATGATGGATGGAGGGAGGCTGAAAGAGACC---

upper sequence: AT2G01130.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 14
aaagagatcttgtcttgaaatcagatggta-tgaagtgttgtgaattctc-gtgtcttctgaaagaccttagaatatgatgtttcgtttttaactttcccagCTCGCAGAAGCCGCAAAGTCCCAGTTTTCACGTGATCACAGTGATCATCTTGCACTTGTTCGGGCATATGAGGGGTGGAAAAAAGCTGAGGAAGAGTCTG
 | ||||  | ||      ||   |||||  | || |  |||   ||||| ||  |        | | ||  ||  | |||| ||   |||    ||   |||| ||||| || |||||  | || ||||| | |||  ||||||| |||||||||||||||||||| |||||||| |||||| | |||||  | ||     
taggagaa-tagtggatgtatagtatggtgctaaaataatgtattttctccgtaacaatatttgggctttgcaac-taatgtatctggtttcttctttgtagCTTGCAGAGGCTGCAAAAGCTCAATTTTCTCATGACTACAGTGACCATCTTGCACTTGTTCGGGCTTATGAGGGCTGGAAAGATGCTGAAAAGGACCAAA


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcgtgtcttctgaaagaccttagaatatgatgtttcgtttttaactttcccagCTCGCAGAAGCCGCAAAGTCCCAGTTTTCACGTGATCACAGTGATCATCTTGCACTTGTTCGGGCATATGAGGGGTGGAAAAAAGCTGAGGAAGAGTCTG
                                        ttttaac  putative branch site (score: 2)
                                       tttttaactttccc  CT-rich tract
                                       tttttaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagagatcttgtcttgaaatcagatggtatgaagtgttgtgaattctcgtgtcttctgaaagaccttagaatatgatgtttcgtttttaactttcccagCTCGCAGAAGCCGCAAAGTCCCAGTTTTCACGTGATCACAGTGATCATCTTGCACTTGTTCGGGCATATGAGGGGTGGAAAAAAGCTGAGGAAGAGTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
aaagaga
- - - - - - - - gaaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaagac