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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgcagcaaatctgttgggtcttgttctgttttgtttcttcaactcaaaatacattgttgtcgataattttttcgggttttcttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G23310.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
gtaggtgcagcaaatctgttgggtcttgttctgttttgtttcttcaactcaaaatacattgttgtcgataattttttcgggttttcttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG
||| |    |   |  |      ||| || |  |      |||| |  |   | || |    | |  |||||||        | |||      |||||||||||||| || ||||||||||||||||| ||||| | ||| ||||| ||||| || ||||| ||||||||||| ||||||
gtaagcatcgtttacataa-atatctcgtgccatgg-acctcttgagtttgcagtaaagaaat-tgaataatttc----aactatct------agGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG

upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
gtaggtgcagcaaatctgttgggtcttgttctgttttgtttcttcaactcaaaatacattgttgtcgataatttttt-cgggttttcttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG
                                    | |   | || |    |   ||||| ||    || | |    |   |    |   |  |||||||| |||||| | ||||||||||| ||||| ||||| | ||| ||||| ||||| |||||||| ||||| |||||  |||||
-----------------------------gtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG

upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 7
-----------------------------------gtaggtgcagcaaatctgttgggtcttgttctgttttgtttcttcaactcaaaatacattgttgtcg--ataattttttcgggttttcttcctat------agGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG
                                     ||   |   ||           |||   |  |||    |  |    ||||   |   || ||| |    |||   |||   | || |  | ||      |||||||| ||||| || || |||||||||||||||||||||| |||||| ||||||||||| || ||||||   ||||||||||||
gtaatatagaatatgttttctacttttctttttcaaaagtctccctaagggccaccccccttcccccttttaaacttattgtgtcaatgcattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG

upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 6
------------gtaggtgcagcaaatctgtt----gggtcttgttctgttttgtttcttcaactca-aaatacattgttgtcgata-attttttcgggttttc--ttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG
            ||   | |      ||||||      ||||     ||           |  || | |||   | |||| || ||  ||| |   |   | ||  | | |  |||||||| || || || || |||||||||||||||||||||| ||| || |||||||||||||| ||||||   ||||||||||||
gtaatatagaatgtgttttctatttttctgtttcaaaagtctccccatggccacccctccccccttataaacttaatgtt-tcaatgcattctgatgttgtgtcaatgcttccagGTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTTTTATTCAGACGAACCAATGTTGACTTGTAGAAAG

upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 6
--------------------------gtaggtgcagcaaatctgttgggtcttgttctgttttgtt--tcttcaactcaaaatacattgttgtcgataattttttcgggttttcttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG
                           |   |     ||||   |||    |   | ||||||  |   |||||  | |    |   |||| | ||| |  || | |   | | | |    |||||||| || || ||||| |||||||||||| | ||||||| ||| || ||||||||||| || ||||||   ||||||||||||
gtattatctaatgtgtttttctacttttccttttcaaaaataccttgaagttccctttgtttttctaaacttcatattatttcaatatgttct-gatgagattgtggtaatgtttcc----agGTGGTCCCTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG

upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 6
---------------------------gtaggtgcagcaaatctgttgggtcttgttctgttttgttt-cttcaactcaaaatacattgttgtcgataattttttcgggttttcttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG
                                | ||  ||  |  |   ||    ||   ||||||   |||||  | |    |   |||| | ||| |  |||| |   | | | |    ||||||||  | || ||||| |||||||||||| | ||||||| ||| || ||||||||||| || ||||||   ||||||||||||
gtattatctaatgtgtttttctagttttccttttcaaaaataccatgaagttccctttgtttttgtaaacttcatattatttcaatatgttct-gatgagattttggtaatgtttcc----agGTGGTCCTTGGGAGCGATAATGTATGAAATGTTAGTGGGGTATCCGCCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG

upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 6
gtaggtgcagcaaatctgttgggtcttgttctgttttgtttcttcaactcaaaatacattgttgtcgataattttttcgggttttcttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG
|| ||| |   ||| ||||       |  | || | |||||   | |      ||   ||       ||||   | |  | ||   || ||  |||||||| |||||||| |||||||| |||||||||||||| | |||||| ||||||||||| || || |||||||||||||| |||
gttggttctctaaaactgtcatcatcttctatgatctgttttccccat---ggattagtttcctcatataaccatct--gtttgaatttctccagGTGGTCTCTTGGTGCTATCATGTACGAAATGCTTGTGGGATATCCACCTTTTTATTCAGATGAACCTATGACAACTTGTAGGAAG

upper sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------gtaggtgcagcaaatctgttgggtcttgttct--------gttttgtttcttcaactcaaaata-----cattgttgtcgataattttttcgggttttcttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG
           || | |      ||||| |    | || | ||        | | |  ||  | | ||  | | |       ||||  || | ||  ||    |    | |||||| |||||||||||||| || |||||||| || ||||| || || |  || |||||||| || ||||| || |||||||||||| | |||
gtatgtgacaagtcgttctcctgaatctttctctttttatccttggctcatgatgtacttgcttagcttgataaagttcttgttgtgttcaaaaaggttgaacgtaagttttcctacagGTGGTCACTTGGAGCAATCATGTACGAGATGCTAGTTGGCTACCCTCCATTTTACTCTGACGAACCTATGACAACTTGTCGCAAG

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|164136199|gb|ES084877.1|ES084877
EST:     GATATGGCATGGAATGTGATTG                         GTGGTCACTTTGGTGCGATCATGTATGAAATGCTTGTGGGG
genomic: GATATGGCATGGAATGTGATTGgtaggtgcag ... cttcctatagGTGGTCACTT-GGTGCGATCATGTATGAAATGCTTGTGGGG
EST: gi|164184297|gb|ES018272.1|ES018272
EST:     GGATATGGCATGGAATGTGATTG                         GTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGG
genomic: GGATATGGCATGGAATGTGATTGgtaggtgcag ... cttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGG
EST: gi|164195097|gb|ES041559.1|ES041559
EST:     GATATGGCATGGAATGTGATTG                         GTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGG
genomic: GATATGGCATGGAATGTGATTGgtaggtgcag ... cttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcaactcaaaatacattgttgtcgataattttttcgggttttcttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG
                                         ttttcttcctat  CT-rich tract
                           ataatttttt  TA-rich tract