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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatattttgttgtctatcttaattttttctagcaagtatagttaaacttaaaaccattaaaaaagtagcactgttctttccattttggatgatatttattctactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG

Basic information

species Arabidopsis thaliana
transcript AT2G20360.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S28_171V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------gtgatattttgttgtctatcttaattttttctagc--aagtatagttaaacttaaaaccattaaaaaagtagc-actgttctttccattttggatgatatttattctactcct----------cagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG---
                                                              ||   || | ||   | |  |     |||| |   ||  ||  ||  | ||| |   |       | | |  | | ||||  ||    |    | |  | |||||    ||          |||||| |||||||||||||||||||||||| || || ||||  ||||||   ||  |    || | |  ||     
gtacgaatcttctcagatcacacctttggttgaagaatgcgtgtgatttagtttttgtcaaagaggattcgatgctcaacacatggaattctggttgaaagatgtttcgaattagagttaggccttgattggtgattcttctcacctgagtaacaggttctcattctgtaactggtataactgcagGAAAAGAGTACGAGACAAGAAATTTCAGCTTCGAGGATGTCAATCATGGAATCTC---AAATCGTATATCTAAG
















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|116387772|gb|EG430364.1|EG430364
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|86048716|gb|DR344471.1|DR344471
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAA
EST: gi|116377195|gb|EG419787.1|EG419787
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|86048712|gb|DR344467.1|DR344467
EST:     TCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTT
genomic: TCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAA-TCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTT
EST: gi|116377193|gb|EG419785.1|EG419785
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|86048720|gb|DR344475.1|DR344475
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGA
EST: gi|86048698|gb|DR344453.1|DR344453
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAG
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAG
EST: gi|86048728|gb|DR344483.1|DR344483
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|86048727|gb|DR344482.1|DR344482
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCG
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCG
EST: gi|86048714|gb|DR344469.1|DR344469
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|86048718|gb|DR344473.1|DR344473
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAA
EST: gi|86048726|gb|DR344481.1|DR344481
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCG
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCG
EST: gi|86048710|gb|DR344465.1|DR344465
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGC
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGC
EST: gi|124738557|gb|EH829811.1|EH829811
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCG
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCG
EST: gi|86048691|gb|DR344446.1|DR344446
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|116377192|gb|EG419784.1|EG419784
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|116377191|gb|EG419783.1|EG419783
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|86048721|gb|DR344476.1|DR344476
EST:     CTCGATTAAGGCTGTCATGGCCAAGGNTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAA
EST: gi|116377190|gb|EG419782.1|EG419782
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|116377199|gb|EG419791.1|EG419791
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|116377200|gb|EG419792.1|EG419792
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|47828656|gb|CK118340.1|CK118340
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|116377196|gb|EG419788.1|EG419788
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|116377187|gb|EG419779.1|EG419779
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
EST: gi|86048696|gb|DR344451.1|DR344451
EST:     CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTG                         GAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA
genomic: CTCGATTAAGGCTGTCATGGCCAAGGCTAATGTCGTTATCAATCTAATTGgtgatatttt ... tactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaaaagtagcactgttctttccattttggatgatatttattctactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG
                                      tttattctactcctc  CT-rich tract
                                atgatatttattcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatattttgttgtctatcttaattttttctagcaagtatagttaaacttaaaaccattaaaaaagtagcactgttctttccattttggatgatatttattctactcctcagGAAGAGAGTACGAGACAAGAAATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG