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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAATgtaagtaatgacctaattgactgtattccattattgtgtagcgatgtttgattctgtatgttattgtatcatttag

Basic information

species Arabidopsis thaliana
transcript AT4G10480.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G10480.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g02960.1 (Oryza sativa), 5'ss of exon 2
GCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAATgtaagtaatgacctaattgact---gtattccattattgtgtagcgatgtttgattctgtatgttat-tgtatcatttag-------
||| || || ||||||||||| ||||| ||||| ||| |||| |||||||||||||| || || |  || |||||  | || ||||||||| | ||||||||||| ||      |  ||        | || |||  |  | |  || |   || |   | | || | || |||   |         
GCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGGAGTCAGCAGGATTACCATCAAGAGAGCCAAGAATgtaagaaactgtgcagctgctgcaaacaatctattcattcgaatggaagacagaattaatgttttctctgaatcccgtgtgtttcag

upper sequence: AT4G10480.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g50360.1 (Oryza sativa), 5'ss of exon 3
GCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAATgtaagtaatgacctaattgac---tgtattccattattgtgtagcgatgtttgattctgtatgttattgtatcatttag-------
||| || || ||||||||||| ||||| ||||| ||| |||| |||||||||||||| || || |  || |||||  | || ||| ||||| | ||||||||||| ||      |  ||        | |  |||  |  | |  || |   || |   | | |   || |||   |         
GCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGGAGTCAGCAGGATTACCATCGAGAGAGCCAAGAATgtaagaaactgtacagctgctgcaaacaatttattcattcgaatggaagacagagttaatgtttctctgaatcccgtgtgtttcag

upper sequence: AT4G10480.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G171466_T01 (Zea mays), 5'ss of exon 2
GCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAATgtaagtaatgacctaattgactg-----tatt-ccattattgtgtagc------gatgtttgattctgtatgttat---tgtatcatttag--------------------------------------------------------------------------------------------
||| ||  | ||||||||||| ||||| ||||| ||| |||| |||||||||||||| || || |  || | |||  | || ||||| ||| | ||||| ||| |||      ||  |   ||     |||| |||  |    | | |      |||   | | | | |||| |     | ||  ||||                                                                                              
GCAGAGCCGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACCGGCGTCACCAGGATAACCATCAAAAGAGCCAAGAACgtacgtatatctatatatatatgccaattattgccacaaggaaggaacacgatagatagctaactttttatgctccgtgtatacaattttacaaacaagatagtagatagatgcccgtgcaatttttagttagctcttgccttctcatattactgtcatgcgtgtctgtctcccttccttcag

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|124788964|gb|EH878643.1|EH878643
EST:     TGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAAT                         GTGTTGTTTGTCATCTCGAAGCCGGATG
genomic: TGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAATgtaagtaatg ... tatcatttagGTGTTGTTTGTCATCTCGAAGCCGGATG
EST: gi|125301050|gb|EL315135.1|EL315135
EST:     TGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAAT                         GTGTTGTTTGTCATCTCGAAGCCGGATGTGTTCAAGAGTCCGAAC
genomic: TGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAATgtaagtaatg ... tatcatttagGTGTTGTTTGTCATCTCGAAGCCGGATGTGTTCAAGAGTCCGAAC
EST: gi|164048330|gb|ES215676.1|ES215676
EST:     CTATCAAGAGATCAAAGAATT                         GTGTTGTTTGTCATCTCGAAGCCGGATGTGTTCAAGAGTCCGAACTCTGA
genomic: CTATCAAGAGATCAAAGAA-Tgtaagtaatg ... tatcatttagGTGTTGTTTGTCATCTCGAAGCCGGATGTGTTCAAGAGTCCGAACTCTGA
EST: gi|86075631|gb|DR371388.1|DR371388
EST:     GAGATCAAAGAAT                         GTGTTGTTTGTCATCTCGAASCCGGATGTGTTCAAGAGTCCGAACTCTGAG
genomic: GAGATCAAAGAATgtaagtaatg ... tatcatttagGTGTTGTTTGTCATCTCGAAGCCGGATGTGTTCAAGAGTCCGAACTCTGAG
EST: gi|116479994|gb|EG522586.1|EG522586
EST:     TGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAAT                         GTGTTGTTTGTCATCTCGAAGCCGGATGTGTTCAAGAGTCCGAACTCTGAG
genomic: TGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAATgtaagtaatg ... tatcatttagGTGTTGTTTGTCATCTCGAAGCCGGATGTGTTCAAGAGTCCGAACTCTGAG
EST: gi|86078942|gb|DR374699.1|DR374699
EST:     TGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAAT                         GTGTTGTTTGTCATCTCGAAGCCGGATGTGTTCAAGAGTCCGAACTCTGAG
genomic: TGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAATgtaagtaatg ... tatcatttagGTGTTGTTTGTCATCTCGAAGCCGGATGTGTTCAAGAGTCCGAACTCTGAG
EST: gi|125001938|gb|EL074207.1|EL074207
EST:     AGTGACTATCAAGAGATCAAAGAAT                         GTGTTGTTTGTCATCTCGAAGCCGGATGTGTTCAAGAGTCCGAACTCTGAG
genomic: AGTGACTATCAAGAGATCAAAGAATgtaagtaatg ... tatcatttagGTGTTGTTTGTCATCTCGAAGCCGGATGTGTTCAAGAGTCCGAACTCTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAGAGTGACTATCAAGAGATCAAAGAATgtaagtaatgacctaattgactgtattccattattgtgtagcgatgtttgattctgtatgttattgtatcatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA