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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgattacttctgtcttatacattgtgcagtcctattttgccagtcttcatatctaaaagaaacatcccttttgttttatctactgtatcttcagCTACTCTGAATCTGAGTACTTTAAGCAAACATTGCGGCAAGGTGCTCCAGCTAAACCTAAAGAGCCTAGAATTCCGCGCATGCCCCAGTT

Basic information

species Arabidopsis thaliana
transcript AT3G06400.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 16
gtaatgattacttctgtcttatacattgtgcagtcctattttgccagtcttcatatctaaaagaaacatcccttttgttttatctactgtatcttcagCTACTCTGAATCTGAGTACTTTAAGCAAACATTGCGGCAAGGTGCTCCAGCTAAACCTAAAGAGCCTAGAATTCCGCGCATGCCCCAGTT
                     ||  |  |  |   |||| |   || |   ||  |||       | |      |  |||| | |  |    ||  ||||||||||| ||||| |||||||||||| || | || |||||||| || || |||||||  || ||  |||||||  | ||||| ||  |
--------------------gtaagtc-tctatctctatgtgtgca-tgcacacgtctggtgctcaaactgacctaattttgtttgtta---ctctagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCGCACCT

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 16
gtaatgattacttctgtcttatacattgtgcagtcctattttgccagtcttcatatctaaaagaaacatcccttttgttttatctactgtatcttcagCTACTCTGAATCTGAGTACTTTAAGCAAACATTGCGGCAAGGTGCTCCAGCTAAACCTAAAGAGCCTAGAATTCCGCGCATGCCCCAGTT
                     || ||  |  |   |||| |   || |   ||  |||       | |      |  |||| | |  |    ||  ||||||||||| ||||| |||||||||||| || | || |||||||| || || |||||||  || ||  |||||||  | ||||| ||  |
--------------------gtaaatc-tctatctctatgtgtgca-tgcacacgtctggtgctgaaactgacctaattttgtttgtta---ctctagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 13
gtaatgattacttctgtcttatacattgtgcagtcctattttgccagtcttcatatctaaaagaaacatccc-ttttgttttatctactgtatcttcagCTACTCTGAATCTGAGTACTTTAAGCAAACATTGCGGCAAGGTGCTCCAGCTAAACCTAAAGAGCCTAGAATTCCGCGCATGCCCCAGTT
                        ||  | |  | |||||||    | | |  || ||  |  |   ||      || ||||| ||     || |  ||||||||||| ||||| |||||||||||| || | || |||||||| ||||| || ||||  || || || |||||  | ||||| || ||
----------------------gtatgctcctcttctatttt-taggccatggta-ctgtagtacttatttgaccttattttaactgtc--atttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 16
gtaatgattacttctgtcttatacattgtgcagtcctattttgccagtcttcatatc-taaaagaaacatcccttttgttttatctactgtatcttcagCTACTCTGAATCTGAGTACTTTAAGCAAACATTGCGGCAAGGTGCTCCAGCTAAACCTAAAGAGCCTAGAATTCCGCGCATGCCCCAGTT
|||||  | | || |   ||   ||   |    |   |||||     | |   |||| |  |||| |  |  |  || | || ||   |   |    || ||||| || ||||| ||||||||||||||| ||||||||||||||||||| ||||  | |||||||||||| ||||||||||||||| |
gtaattgtgaattttcagttgc-caacttatgttataattttatgtttttcattatcatttaagacatgtttccattttcttgtcctttaagt----agTTACTCAGAGTCTGAATACTTTAAGCAAACAATGCGGCAAGGTGCTCCAGCAAAACAAAGAGAGCCTAGAATACCGCGCATGCCCCAGCT

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|116473628|gb|EG516220.1|EG516220
EST:     ATTGTAAGCGACAATTGGAATGATCCCCCCAAGCGGGAGAGAAAGCGCAA                         CTACTCTGAATCTGAGTACTTTAAGCAAACATTGCGGCAAGGTGCTCCAGC
genomic: ATTGTAAGCGACAATTGGAATGATCCCCCCAAGCGGGAGAGAAAGCGCAAgtaatgatta ... gtatcttcagCTACTCTGAATCTGAGTACTTTAAGCAAACATTGCGGCAAGGTGCTCCAGC
EST: gi|116473629|gb|EG516221.1|EG516221
EST:     ATTGTAAGCGACAATTGGAATGATCCCCCCAAGCGGGAGAGAAAGCGCAA                         CTACTCTGAATCTGAGTACTTTAAGCAAACATTGCGGCAAGGTGCTCCAGC
genomic: ATTGTAAGCGACAATTGGAATGATCCCCCCAAGCGGGAGAGAAAGCGCAAgtaatgatta ... gtatcttcagCTACTCTGAATCTGAGTACTTTAAGCAAACATTGCGGCAAGGTGCTCCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagtcttcatatctaaaagaaacatcccttttgttttatctactgtatcttcagCTACTCTGAATCTGAGTACTTTAAGCAAACATTGCGGCAAGGTGCTCCAGCTAAACCTAAAGAGCCTAGAATTCCGCGCATGCCCCAGTT
           atctaaa  putative branch site (score: 3)
                                              tatcttc  putative PPT
         atatctaaaagaaa  TA-rich tract