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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacaaacagtccatcaaactattgcacttgtatccctgttttactcaattttctcactctttcgttttgataaatgtttgtgtaaccactcgtttgtttgcagTTATTCTGGAACACTTTGACCAGGTGATAGGTGACTGCTTCATGGATTGTGTCAATTGTCTCATCAGGTTTGCCAATAACAAAGCTTCAGACCGGATAAG

Basic information

species Arabidopsis thaliana
transcript AT3G43300.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G43300.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 22
gtga-caaacagtccatcaaactattgcacttgtatccctgttttactcaattttctcactctttc-----gttttgataaatgtttgtgt-aaccactcgtttgtttgcagTTATTCTGGAACACTTTGACCAGGTGATAGGTGACTGCTTCATGGATTGTGTCAATTGTCTCATCAGGTTTGCCAATAACAAAGCTTCAGACCGGATAAG
|| |  ||  | |  ||  | |||   |        || |      || |  |    ||  || ||      ||||  |   ||  | ||| ||  |  || |   || |||||||  ||||||| ||||| || ||  | ||||| |||||||||||||||||||| ||||| ||  | ||||| ||||||||     |    ||||| ||
gtaaataaggaatttatatagctagctcgtaaagtaccttacccaccttatatcctacaacctatcttgaaattttattggctgactttgtgaatgaaacggtgtcttacagTTATCTTGGAACATTTTGATCAAGTCGTTGGTGATTGCTTCATGGATTGTGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAG

upper sequence: AT3G43300.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 24
gtgacaaacagtccatcaaactattgcacttgtatccctgttttactcaattt--tctcactctttcgttttgataaatgtttgtgtaaccactcgtttgtttgcagTTATTCTGGAACACTTTGACCAGGTGATAGGTGACTGCTTCATGGATTGTGTCAATTGTCTCATCAGGTTTGCCAATAACAAAGCTTCAGACCGGATAAG
               | | | || |   ||| | ||  ||| ||  | | |    ||| | |||    ||    |    || | | ||||   | |    ||| |||| ||  | ||||||||||| || ||  | || ||||| ||||||||||| || |||||||| |||||||||||||| || ||| ||||| | || || ||
--------------gtaagaataattttctt-tgtctttgtctttgttattgcagtctaagtctactattgcatttgtggtgtatctaacacatggacattttacagTCATCTTAGAACACTTTGATCAAGTAGTGGGAGACTGTTTCATGGATTGCGTGAATTGTCTGATCAGGTTTGCCAACAATAAAACTTCACATCGTATTAG

upper sequence: AT3G43300.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 24
gtgacaaacagtccatcaaactattgcacttgtatccctgttttactcaattt---tctcactctttcgttttgataaatgtttgtgtaaccactcgtttgtttgcagTTATTCTGGAACACTTTGACCAGGTGATAGGTGACTGCTTCATGGATTGTGTCAATTGTCTCATCAGGTTTGCCAATAACAAAGCTTCAGACCGGATAAG
               | | | || |   ||| | ||  |||  |   || | |   ||| | |||    ||    |    || | | ||||   | |    ||| |||| ||  | ||||||||||| || ||  | || ||||| ||||||||||| || |||||||| |||||||||||||| || ||| ||||  | || || ||
--------------gtaagaataattttctt-tgtctgtgtcat-tgcagtctaagtctaagtctactattgcatttgtggtgtatctaacgcatggacattttacagTCATCTTAGAACACTTTGATCAAGTAGTGGGAGACTGTTTCATGGATTGCGTGAATTGTCTGATCAGGTTTGCCAACAATAAAACTTCGCATCGTATTAG

upper sequence: AT3G43300.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 24
gtgacaaacagtccatcaaactattgcacttgtatccctgttt-tactcaattttctcactctttcgttttgataaatgtttgtgtaaccactcgtttgtttgcagTTATTCTGGAACACTTTGACCAGGTGATAGGTGACTGCTTCATGGATTGTGTCAATTGTCTCATCAGGTTTGCCAATAACAAAGCTTCAGACCGGATAAG
|| | ||   | |  |     | || |   ||| |   |  || | |||||| || ||    ||| ||  |     ||     | ||||     || | |||||||||||  |||| |||||||| |||||  | || |||||||| ||||| |||||||| ||||||||  | ||| ||||||| |||  |||  | || || ||
gtaagaacatgccatttttcttctttcttatgtgtttttacttattctcaatgttttcttctttttgtcatttctgatac--atttaacacgaagtatatttgcagTTATCTTGGAGCACTTTGATCAGGTAGTTGGAGACTGCTTTATGGACTGTGTCAACTGTCTCATTGGCTTTTCCAATAATAAAAGTTCCCATCGCATCAG

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|125129593|gb|EL173277.1|EL173277
EST:     TGACGAAGTTGAATCGATAGTTGAAAAATCATTTGAGAATGTTGAGCAAG                         TTATTCTGGAACACT
genomic: TGACGAAGTTGAATCGATAGTTGAAAAATCATTTGAGAATGTTGAGCAAGgtgacaaaca ... ttgtttgcagTTATTCTGGAACACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctcactctttcgttttgataaatgtttgtgtaaccactcgtttgtttgcagTTATTCTGGAACACTTTGACCAGGTGATAGGTGACTGCTTCATGGATTGTGTCAATTGTCTCATCAGGTTTGCCAATAACAAAGCTTCAGACCGGATAAG
                                        ctcgttt  CT-rich tract
                ttttgataaatgttt  TA-rich tract