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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCTCAAGACACTTGATCGGTACCAGAAATGCAGCTATGGATCCATTGAAGTCAACAACAAACCTGCCAAAGAACTTGAGgtgttcttaattcaaatactattttagattcctatcatatcatttcaagaaagatcttttttaaaagtttgttttcgtgaaatatttcag

Basic information

species Arabidopsis thaliana
transcript AT5G15800.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G15800.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA18G50900.1 (Glycine max), 5'ss of exon 2
CATGCTCAAGACACTTGATCGGTACCAGAAATGCAGCTATGGATCCATTGAAGTCAACAACAAACCTGCCAAAGAACTTGAGgtgt-tcttaatt-caaatactattttagattcctatcatatcat-ttcaagaaagatcttttttaaaagtttgttttcgtgaaatatttcag-------------------------------------------------------------------
||||||||| ||||||||  ||||||||||||||||||||||  |  | ||||| | |||   |||||||||||| || ||||| | |   || | ||  |  |  | |  | |   || | | | | |   |||||| || | |   ||| | |  | |  | || ||| | |                                                                    
CATGCTCAAAACACTTGAAAGGTACCAGAAATGCAGCTATGGTGCTGTGGAAGTTAGCAA---ACCTGCCAAAGAGCTCGAGgtatatagcaactgcagctcttgctgtttactggcattacagcttatctcagaaagttcatataggaaactataatataattaattatgtaacataccatatatgtagtttttctttattattgttacatctttcaattctggttacttttcatttgtag

upper sequence: AT5G15800.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA08G27670.1 (Glycine max), 5'ss of exon 2
CATGCTCAAGACACTTGATCGGTACCAGAAATGCAGCTATGGATCCATTGAAGTCAACAACAAACCTGCCAAAGAACTTGAGgtgttcttaattcaaatactattttagattcctatcatatcattt---caagaaagatcttttttaaaagtttgttttcgtgaaatatttcag------------------------------------------------------------------------------
||||||||| ||||||||  |||||||||||||||| |||||  |  | ||||| | |||   |||||||||||| || ||||| |    | | ||  |  |  | |  |||   || |  |   ||      ||||| || | |   ||| | |  | |  | || ||| | |                                                                               
CATGCTCAAAACACTTGAAAGGTACCAGAAATGCAGTTATGGTGCTGTGGAAGTTACCAA---ACCTGCCAAAGAGCTCGAGgtttagcaactgcagctgttgctctttattggcattacgtagcttatctcggaaagttcatataggaaaatataatataattaactatataacatatacaatatatgtatatatagtttttctttgttattgttacatcttgcaattcttgttatttttcatttgtagcag
















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|164226602|gb|ES168816.1|ES168816
EST:     CCAAAGAACTTGAG                         AACAGCTACAGAGAATATCTGAAGCTTAAGGGTAGATATGAGAACCTTCAA
genomic: CCAAAGAACTTGAGgtgttcttaa ... aatatttcagAACAGCTACAGAGAATATCTGAAGCTTAAGGGTAGATATGAGAACCTTCAA
EST: gi|47831874|gb|CK121558.1|CK121558
EST:     GCAGCTATGGATCCATTGAAGTCAACAACAAACCTGCCAAAGAACTTGAG                         AACAGCTACAGAGAATATCTGAAGCTTAAGGGTAGATATGAGAACCTTCAA
genomic: GCAGCTATGGATCCATTGAAGTCAACAACAAACCTGCCAAAGAACTTGAGgtgttcttaa ... aatatttcagAACAGCTACAGAGAATATCTGAAGCTTAAGGGTAGATATGAGAACCTTCAA
EST: gi|19878650|gb|AU239481.1|AU239481
EST:     GCAGCTATGGATCCATTGAAGTCAACAACAAACCTGCCAAAGAACTTGAG                         AACAGCTACAGAGAATATCTGAAGCTTAAGGGT-GATATGAGAACCTTCAA
genomic: GCAGCTATGGATCCATTGAAGTCAACAACAAACCTGCCAAAGAACTTGAGgtgttcttaa ... aatatttcagAACAGCTACAGAGAATATCTGAAGCTTAAGGGTAGATATGAGAACCTTCAA
EST: gi|86073095|gb|DR368852.1|DR368852
EST:     GCAGCTATGGATCCATTGAAGTCAACAACAAACCTGCCAAAGAACTTGAG                         AACAGCTACAGAGAATATCTGA-GCTTAAGGGTAGATATGAGAACCTTCA-
genomic: GCAGCTATGGATCCATTGAAGTCAACAACAAACCTGCCAAAGAACTTGAGgtgttcttaa ... aatatttcagAACAGCTACAGAGAATATCTGAAGCTTAAGGGTAGATATGAGAACCTTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCTCAAGACACTTGATCGGTACCAGAAATGCAGCTATGGATCCATTGAAGTCAACAACAAACCTGCCAAAGAACTTGAGgtgttcttaattcaaatactattttagattcctatcatatcatttcaagaaagatcttttttaaaagtttgttttcgtgaaatatttcag

- - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC