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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatgtcttaattctgttaacaaaagcatgtaaaattcccttagttttaactattaaagtaagtcagacttattcttctgtcttttcttttctcaaccagAGCGCATCATGGTTTTGGATGGGTTGGAGAATGGGCAAGTTCCGG

Basic information

species Arabidopsis thaliana
transcript AT1G34320.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G34320.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G148773_T01 (Zea mays), 3'ss of exon 10
------tgatgtcttaattctgttaacaaaagcatgtaaaattcccttagttttaactattaaagtaagtcagacttattcttctgtcttttcttttctcaaccagAGCGCATCATGGTTTTGGATGGGTTGGAGAATGGGCAAGTTCCGG
      | |  | ||||||   || | |   ||||| |||||  | |  |  ||  ||  | |      |  |  |  | | | | |  |    | ||   || || || ||||||||||| || ||||||||||| ||||||||| ||||
gtaatctaaattattaattgccttcata---gcatgcaaaatagcttggggctt--ctgcttatccctttttg-ttactgcatttttgatgatctgtccatacaagGGCTCATCATGGTTTCGGTTGGGTTGGAGAGTGGGCAAGTACCGG

upper sequence: AT1G34320.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G31400.1 (Glycine max), 3'ss of exon 13
tgatgtcttaattctgttaacaaaagcatgtaaaattcccttagt-tttaactattaaagtaagtcagacttattcttctgtcttttcttt--tctcaaccagAGCGCATCATGGTTTTGGATGGGTTGGAGAATGGGCAAGTTCCGG
   |  |||  || ||||  |         | || | || |||   | ||  | ||    |   ||| | |||   || | | |||   ||    | |  |||||| |||||||| ||||||||||||||||||||||| |   | ||
-attagcttttttatgttctcttctattattcaattaccattaacctctatatgttctgctc--tcaaatttaacattttctttttcacttggattaattcagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAACACAGG

upper sequence: AT1G34320.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 13
--tgatgtcttaattctgttaacaaaagcatgtaaaattcccttagttttaactattaaagtaagtcagacttattcttctgtcttttcttttctcaacc-agAGCGCATCATGGTTTTGGATGGGTTGGAGAATGGGCAAGTTCCGG
   ||| | ||  ||    | |   ||  |     ||   |   |  ||   || | ||||    |||   | |   |    | ||  |||   | ||   ||||| |||||||| ||||||||||||||||||||||| | | | ||
ttcgatatgttcttttctattattcaattaccattaacctctacatgttcttctctcaaagc---tcaatttaaccatatctttttcacttggattaatttagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG

upper sequence: AT1G34320.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S54_228V6.1 (Physcomitrella patens), 3'ss of exon 10
--tgatgtcttaatt-ctgttaacaaaagcatgtaaaattcccttagttttaactattaaagtaagtcagacttattcttctgtcttttcttttctcaac-cagAGCGCATCATGGTTTTGGATGGGTTGGAGAATGGGCAAGTTCCGG
  |  |||  || || ||| ||      | |||   |  |   || ||| ||    | |||  | |   ||  |  | |  ||  ||   ||   |   | |||   ||||||||| ||||||||||||||||| ||||| | | | ||
tcttgtgttatagttactgctatttcgtgaatgagtatcttgtttggttatac---tcaaatcatggacgatct-ctttaatgctttgaattgggttgccacagGAAGCATCATGGCTTTGGATGGGTTGGAGAGTGGGCGAATGCTGG

upper sequence: AT1G34320.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ35129 (Selaginella moellendorffii), 3'ss of exon 9
tgatgtcttaattctgttaacaaaagcatgtaaaattcccttagttttaactattaaagtaagtcagacttattcttctgtcttttcttttctcaacc---agAGCGCATCATGGTTTTGGATGGGTTGGAGAATGGGCAAGTTCCGG
                                        ||| ||   |   | ||  |       ||     |     || | | |||| |||| |   ||||| ||||| || |||||||||||||| |||||||||| ||| ||
---------------------------------------gttaattcatatggtcaagctcgtgtgaacgctaaccagcctcctcttttttatcaatctctagAGCTCATCACGGATTTGGATGGGTTGGCGAATGGGCAAATTCTGG

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|124753396|gb|EH843526.1|EH843526
EST:     ATGGAAAAAACATTGCAGTGGCTTGTTCCTGTTGCTACAAACACCACCAA                         AGCGCATCATGGTTTTGGATGGGTTGGAGAATGGGCAAGTTCCGG
genomic: ATGGAAAAAACATTGCAGTGGCTTGTTCCTGTTGCTACAAACACCACCAAgtaagcttct ... tctcaaccagAGCGCATCATGGTTTTGGATGGGTTGGAGAATGGGCAAGTTCCGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaactattaaagtaagtcagacttattcttctgtcttttcttttctcaaccagAGCGCATCATGGTTTTGGATGGGTTGGAGAATGGGCAAGTTCCGG
 ttttaac  putative branch site (score: 2)
                       cttattcttctgtctt  putative PPT
      tattaaagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatgtcttaattctgttaacaaaagcatgtaaaattcccttagttttaactattaaagtaagtcagacttattcttctgtcttttcttttctcaaccagAGCGCATCATGGTTTTGGATGGGTTGGAGAATGGGCAAGTTCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - caaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagtaag