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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattctctttgtcgaaaatcttgttgatcctaaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA

Basic information

species Arabidopsis thaliana
transcript AT1G17720.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 6
ttattctctttgtcgaaaatcttgttgatcctaaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaat-tgttaca----gTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
 | |     || ||  ||    |  |  | |    ||    |     ||||      |  ||  | |   | ||||     |||| | || | | |||||    ||||||| || || |  || || || |||||||||||| ||||||| |||||  |||||||||||||||| || || |||||||||||||| |||||  ||
ctgtgtgagttctctgaacctataatactacctgcttctgta-----tattttcaaatcatgagcatgaagctaataccatgttctcatattgttttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAACCAAAGCTTTAATATTGTTGATGTGAAGCCTGCA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 6
ttattctctttgtcgaaaatcttgttgatcctaaatttcacaacttgtattgcattgtttt--gttccttgtggtaatgaatcgtt-----cccttaattgtt---acagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
        ||||  ||    | | |      || |||  |  |  |||| || |   |||   |||   ||| || |   || |||     | |||  || ||   ||||||| || || || || || || || |||||| ||||  ||||||| ||||||||||||||||||||||| ||||| || ||| |||||||||| || |||
--------tttgctgatgtgcatctca--tatacattcgattagatgtaatgtaccctttcgagttttatgtagtgacatattgttgcctgctcttttttttttcgacagTGATGGTGAGACTTTCATATCAGCAGATGATTTGCGGATAAATCTTTGGAATTTGGAAATTAGCAACCAAAGTTTTAACATTATTGATGTTAAACCTACA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 6
ttattctctttgtcgaaaatcttgttgatcctaaatttcaca-acttgt--attgcattgttttgt--tccttgtggtaatgaa------tcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
         || ||   | | ||  |     || ||| || | |||| |  | ||   |  |||||   | ||||| | ||         |  |||  ||||||||  |||||| || || || |  || || || |||||||||||  ||||||| ||||||||||| || |  |||||||| |||||||||||||| || |||||  ||
---------ttatctgcagtttttctacctgtatattccatatactttttcaatgatctaatttgtgaacattgtgctgatttgcttctctttttcatttaattgt--cagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 6
ttattctctttgtcgaaaatcttgttgatcctaaat-ttcacaact-tgtattgcattgttttgttcc-ttgtggta---atgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
    |  ||   | | |  |||| |  ||| ||||| |   |  |  | | ||| |||||  | ||   | ||| ||   || | | ||   ||| |||   ||||||| || || || ||||| || ||||||||| ||||  ||||||| |||||||||||||| ||||| || |||||||||||| ||||||||||||| |||
----ttgctgatttgcacctcttat--atcttaaatgtatgctgccattttttgtattgtcctattgggtagtgatatatattatttgtaatctttatttcaacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 6
ttattctctttgtcgaaaatcttgttgatcctaaatttca---caact-tgtattgc-attgttttgttccttgtggtaatgaat----cgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
        | ||| |   || |||    || |  |||  |    |||| |   |||| ||| ||||||     || |||||  ||     ||  |||  |||   ||||||| || || || ||||| || ||||||||| ||||  ||||||| |||||||||||||| ||||| || |||||||||||| ||||||||||||| |||
--------tatgttgctgat-ttgcccctcatgtattgtagcttaactgtactttgccatttttttgtattgggtagtaatatatatattgtaacctctatttccacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
----ttattctctttgtcgaaaatcttgttg-atcctaaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaatt--gttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
    | | |   | || |  |  | || ||| ||| || ||||  |  | ||  ||  |||  | ||      ||| ||     || |  | ||  ||   | |||| || |||||||| || || || || |||||||||||| |||| || |||||||| ||||||||||| ||||| || || ||||||||||| || ||  ||
tgaatgagttaatgtggctgagttttttttggatcttatattttgctgcctgggtt-tattactatg------gtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
----ttattctctttgtcgaaaatcttgttgatcctaaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
     | |   | |  |           ||  |  | |||||||    ||       | || |    |     ||||  |   | | ||    |  | || ||| || || ||||| || || || || |||||||||||| ||||||| |||||  ||||||||||||| || ||||| |||||||||||||| |||||  ||
ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctc----atatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
ttattctctttgtcgaaaatcttgttgatcct----aaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
|   |   |||||  | | | || ||  |  |    || ||||| |  ||       | || |    |     ||||  |   | | ||    |  | ||  || || || ||||| || || || ||||||||| ||||| ||||||| |||||  ||||||||||||| || ||||| |||||||||||||| |||||  ||
tacgtgattttgtgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctc----atattttctagCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
---ttattctctttgtcgaaaatcttgttgatcctaaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
    | |   | || |       ||| ||  |  |   | |  ||   | |  || | | |  |     |||   ||  | ||  |||   ||  || ||  | || |||||||| || || || ||||||||| | ||| ||||||| |||||  ||||||||||||| || ||||| |||||||||||||| |||||  ||
ttcatgtatgcattttttgcgcccttatttttgtttg-tctatcatgcttttctgaaatctgatcaaatttggactatggtatgtttcaaatatctgcta--gCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
----ttattctctttgtcgaaaatcttgttgatcctaaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
     | |    ||| |    |  |||  |  |  |   | ||| |  ||    || | | |  |     |||   ||  | ||  |||   ||  || ||  | || || ||||| || || || ||||||||| | ||| ||||||| |||||  ||||||||||||| || ||||| |||||||||||||| |||||  ||
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttc--tgaaatctgatcaaatttggactatggtatgtttcaaatatctgcta--gCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 6
ttattctctttgtcgaaaatcttgttgatcctaaatttcacaacttgtattgcattgttttg-ttccttgtggtaatg--aatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
  |    || |   | |||   || | ||  |||  ||    | || | ||   | | |  | ||   ||   |  ||   || ||| |  |   | |  |||||| || ||||| ||||| || ||||||||||||||| |||| || ||||| ||||||||||||||||| || ||||||||||||||||| |||||  ||
-gaaagactattatggaaacaatgctaatggtaa-cttgtttatttctcttatttgggtacgatttagtgaaattttgctgattgtttctctctctctc-cagTGATGGTGAAACATTTATATCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCA

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|116478423|gb|EG521015.1|EG521015
EST:     GTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAG                         TGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAA
genomic: GTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAGgtaatcgttt ... attgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtattgcattgttttgttccttgtggtaatgaatcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA
                                        ccttaat  putative branch site (score: 4)
                                          ttaattgtta  TA-rich tract