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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtggaaattcttatagcaggaacataactaatccttaactatttgtgttcccagaatttgactttctgtctgatttttggatagGCCAAGTGCCTGGAAACGGGTGAACAAGTTGCAATTAAGAAGGTTCTGCAGGATAAAAGATACAAGAACAGAGAACTTCAGATCATGCGTTTGCAAGACC

Basic information

species Arabidopsis thaliana
transcript AT4G00720.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 4
------------gtaggtggaaattct-tatagcagg-----aacataactaatcctta-actatttgtgttcccagaatttgactttctgtctgatttttggatagGCCAAGTGCCTGGAAACGGGTGAACAAGTTGCAATTAAGAAGGTTCTGCAGGATAAAAGATACAAGAACAGAGAACTTCAGATCATGCGTTTGCAAGACC
              |  | |  ||||| ||| ||          ||| |   |   ||| | |||||| |     ||   |||||    | | ||||      | ||||||||||| ||||||| || ||    ||||| ||||||||||||||||| ||||||||||| ||||||||||| || || |  ||||   |||  ||||
gtatattatttcacattttgccattctgtatcgctactcctcgtcatgatggaaatttacaatatttgggcataaagttattgaccagttat-tgatac--aaacagGCCAAGTGCTTGGAAACTGGAGAGACTGTTGCCATTAAGAAGGTTCTGCAAGATAAAAGATATAAGAACAGAGAGCTCCAAACAATGCAACTGCTTGACC

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 4
gtaggtggaaat--tctt---atagcaggaacataactaatccttaactatttgtgttcccagaatt-------tgactttctgtctgatttttgga---tagGCCAAGTGCCTGGAAACGGGTGAACAAGTTGCAATTAAGAAGGTTCTGCAGGATAAAAGATACAAGAACAGAGAACTTCAGATCATGCGTTTGCAAGACC
|||  ||||| |  ||||   ||| |  |     || |   | ||   || || |      |  |||       |   ||| ||| | |||||   |    |||| || ||||| ||||| ||||||  ||| |||||||||||||| ||||||||||| ||||||||||| |||||||| || || |||||  | |  ||||
gtacttggaattgatcttgatataccttgtgagcaattggcctttgggtaattttccagataatattgttctcatttttttatgttttattttgacaatgcagGCTAAATGCCTAGAAACAGGTGAAGCAGTGGCAATTAAGAAGGTGCTGCAGGATAAGAGATACAAGAATAGAGAACTCCAAATTATGCGCGTACTTGACC

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 3
------gtaggtggaaattcttatagcaggaacataac--taatccttaactatttgtgt--tcccagaatttgactttctgtctgatttttg--gatagGCCAAGTGCCTGGAAACGGGTGAACAAGTTGCAATTAAGAAGGTTCTGCAGGATAAAAGATACAAGAACAGAGAACTTCAGATCATGCGTTTGCAAGACC
      |  |  | || | |  || |    |   | ||  ||| |     ||  | | |   |  | |  | |||||| |    | || | ||  |  |||| || ||| | ||||| || ||    || || || ||||| || |||||||| ||||||||||||||  |||| || |||||||||||  ||   ||||
tacgttgcggaggaaagtccaaatggttatatgtttaccctaacctcatgctggtagagggatagctgtgtctgacttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGCTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC

upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 3
----------gtaggtggaaattcttatagcaggaacataactaatccttaac-tatttgtgttcccagaa--tttgactttctgtctgatttt-tggatagGCCAAGTGCCTGGAAACGGGTGAACAAGTTGCAATTAAGAAGGTTCTGCAGGATAAAAGATACAAGAACAGAGAACTTCAGATCATGCGTTTGCAAGACC
          | ||   || ||     |     |  |||   | |   | ||  |  | |   |    ||   | |||      |  | ||||| | |  |||| || ||| | || |  || |||   || || ||||||||||| || ||||| || |||||||||||| |||||||||||||||||||  |||  || |
taacttcactggagccagacatggggctgatctgtccatg--tgacgttcaaggtggtagaactaggggatgttctgatcgcgagggtaattttgttgtcagGCAAAATGCATAGAGAGCGGAGAAACTGTGGCTATTAAGAAGGTGCTTCAGGACAAGAGATACAAGAACCGAGAACTTCAGATCATGCGGCTGCTGGAGC

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|124740973|gb|EH832135.1|EH832135
EST:     ACATGGCCCAGCGAGTGGTTGGAACCGGCTCATTCGGAGTAGTGTTCCAG                         GCCAAGTGCCTGGA
genomic: ACATGGCCCAGCGAGTGGTTGGAACCGGCTCATTCGGAGTAGTGTTCCAGgtaggtggaa ... ttttggatagGCCAAGTGCCTGGA
EST: gi|124899822|gb|EH974440.1|EH974440
EST:     ACATGGCCCAGCGAGTGGTTGGAACCGGCTCATTCGGAGTAGTGTTCCAG                         GCCAAGTGCCTGGAAACGGGTGAACAAGTTGCAATTAAGAAGGTTCTGCAG
genomic: ACATGGCCCAGCGAGTGGTTGGAACCGGCTCATTCGGAGTAGTGTTCCAGgtaggtggaa ... ttttggatagGCCAAGTGCCTGGAAACGGGTGAACAAGTTGCAATTAAGAAGGTTCTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatccttaactatttgtgttcccagaatttgactttctgtctgatttttggatagGCCAAGTGCCTGGAAACGGGTGAACAAGTTGCAATTAAGAAGGTTCTGCAGGATAAAAGATACAAGAACAGAGAACTTCAGATCATGCGTTTGCAAGACC
                                            ttttt  CT-rich tract
     ttaactattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtggaaattcttatagcaggaacataactaatccttaactatttgtgttcccagaatttgactttctgtctgatttttggatagGCCAAGTGCCTGGAAACGGGTGAACAAGTTGCAATTAAGAAGGTTCTGCAGGATAAAAGATACAAGAACAGAGAACTTCAGATCATGCGTTTGCAAGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA