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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataccctaacggaatggctgttattcttgatccatggcatccttcaaaacttcgtttctgatttttatatatcctgtagGGTGAAGATGTTGCTTTTGAACCGTCAAAGCTTCTGTGGCTTATCCAGCGTGATTTTCTGC

Basic information

species Arabidopsis thaliana
transcript AT2G38840.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 8
------gtataccctaacggaatggctgttattcttgatcca----tggcatccttcaaaacttcgtttctgatttttatatatcctgt-agGGTGAAGATGTTGCTTTTGAACCGTCAAAGCTTCTGTGGCTTATCCAGCGTGATTTTCTGC
       |  | |   | |||         ||  ||||   |    | | || ||   || ||  |||  |||  | | | | |  | | ||||  |||||||||||||||||||  |||||||||| |||||||||||| | ||||| ||||
gtaatgttccatctccatggatctatctggataattgaaatagaaatagaattctgtgaagct--gttaatgacatatgtttgttttttcagGGGCAAGATGTTGCTTTTGAACCAGCAAAGCTTCTTTGGCTTATCCAGAGGGATTTCCTGC

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os07g08400.1 (Oryza sativa), 3'ss of exon 8
gta-taccctaacggaatggctgttattcttgatccatggcatccttcaaaacttcgtttctgatttttatatatcctgtagGGTGAAGATGTTGCTTTTGAACCGTCAAAGCTTCTGTGGCTTATCCAGCGTGATTTTCTGC
||| |||   | |  ||  | |   ||| || |  | | | | |  |  |        ||    |  || | |   ||||||||  |||||||||||||||| ||  |||| || ||||||||||||||| | ||||| || |
gtaatacttaaccttaagtgttagaattatttaaac-tagaaccact--atgtcaaagttacagtgcttgtct---ctgtagGGGCAAGATGTTGCTTTTGAGCCAGCAAAACTACTGTGGCTTATCCAGAGGGATTTCCTCC

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G305254_T04 (Zea mays), 3'ss of exon 7
-------------------------------------------------------------------------------------------------------------gta-taccctaacggaatggctgttattcttgatccatggcatccttcaaaacttcgtttctgatttttatatatcctgtagGGTGAAGATGTTGCTTTTGAACCGTCAAAGCTTCTGTGGCTTATCCAGCGTGATTTTCTGC
                                                                                                             ||| ||| | |     |||  |  ||    ||    || | | | |  | |  ||  |    ||  |   ||| | |   ||||  |||||||||||||||| ||  |||||||||| |||||||||||| | ||||| || |
tttgctcatttcttttgtgcctttctgtttccatataatcattttgatctggaacactaacatttatcctttttttgttatatgctgcacttttgtgagcagagtgaaggtaatactccagtttcatgaattataaggctgtaaaataggaacatggatatttttttgatggaaatgcttatCTTC---AGGGGCAAGATGTTGCTTTTGAGCCAGCAAAGCTTCTCTGGCTTATCCAGAGGGATTTCCTCC

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G321413_T01 (Zea mays), 3'ss of exon 1
---------------------gta-taccctaacggaatggctgttattcttgatccatggcatccttcaaaacttcgtttctgatttttatatatcctgtagGGTGAAGATGTTGCTTTTGAACCGTCAAAGCTTCTGTGGCTTATCCAGCGTGATTTTCTGC
                     |||  ||   |   |  || ||  ||  | ||  | || | | | |  | |  ||  |    ||  |   | | || |  ||||  |||||||||||||||| ||  |||||||||| |||||||||||| | ||||| || |
atgtttgtgagcagagtgaaggtaacactgcatttgcgtgacttataagcctg--caataggaacatggatagttttttaatggaaatgcttgtttctt-cagGGGCAAGATGTTGCTTTTGAGCCAGCAAAGCTTCTCTGGCTTATCCAGAGGGATTTCCTCC

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G305254_T07 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------------------------------------------------gta-taccctaacggaatggctgttattcttgatccatggcatccttcaaaacttcgtttctgatttttatatatcctgtagGGTGAAGATGTTGCTTTTGAACCGTCAAAGCTTCTGTGGCTTATCCAGCGTGATTTTCTGC
                                                                                                              ||| ||| | |     |||  |  ||    ||    || | | | |  | |  ||  |    ||  |   ||| | |   ||||  |||||||||||||||| ||  |||||||||| |||||||||||| | ||||| || |
gtttgctcatttcttttgtgcctttctgtttccatataatcattttgatctggaacactaacatttatcctttttttgttatatgctgcacttttgtgagcagagtgaaggtaatactccagtttcatgaattataaggctgtaaaataggaacatggatatttttttgatggaaatgcttaTCTTC---AGGGGCAAGATGTTGCTTTTGAGCCAGCAAAGCTTCTCTGGCTTATCCAGAGGGATTTCCTCC

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G019361_T01 (Zea mays), 3'ss of exon 7
--------------------------------------------------------------------------------------------------gta-taccctaacggaatggctgttattcttgatccatggcatccttcaaaacttcgtttctgatttttatatatcctgtagGGTGAAGATGTTGCTTTTGAACCGTCAAAGCTTCTGTGGCTTATCCAGCGTGATTTTCTGC
                                                                                                  |||  ||   |   |  || ||  ||  | ||  | || | | | |  | |  ||  |    ||  |   | | || |  ||||  |||||||||||||||| ||  |||||||||| |||||||||||| | ||||| || |
ttttcgtgcctttctgtttggttataatcattttgatctggaaaactaacatttattctttttttgttatatgctgcatgtttgtgagcagagtgaaggtaacactgcatttgcgtgacttataagcctg--caataggaacatggatagttttttaatggaaatgcttgtttctt-cagGGGCAAGATGTTGCTTTTGAGCCAGCAAAGCTTCTCTGGCTTATCCAGAGGGATTTCCTCC

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G019361_T02 (Zea mays), 3'ss of exon 7
-------------------------------------------------------------------------------------------------------gta-taccctaacggaatggctgttattcttgatccatggcatccttcaaaacttcgtttctgatttttatatatcctgtagGGTGAAGATGTTGCTTTTGAACCGTCAAAGCTTCTGTGGCTTATCCAGCGTGATTTTCTGC
                                                                                                       |||  ||   |   |  || ||  ||  | ||  | || | | | |  | |  ||  |    ||  |   | | || |  ||||  |||||||||||||||| ||  |||||||||| |||||||||||| | ||||| || |
ttcatttttcgtgcctttctgtttggttataatcattttgatctggaaaactaacatttattctttttttgttatatgctgcatgtttgtgagcagagtgaaggtaacactgcatttgcgtgacttataagcctg--caataggaacatggatagttttttaatggaaatgcttgtttctt-cAGGGGCAAGATGTTGCTTTTGAGCCAGCAAAGCTTCTCTGGCTTATCCAGAGGGATTTCCTCC

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv07s0141g00110.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------------------gtataccctaacggaatggctgttat---tcttgatccatg-gcatccttc----aaaact---tcgtttctgatttttatat--atcctgtagGGTGAAGATGTTGCTTTTGAACCGTCAAAGCTTCTGTGGCTTATCCAGCGTGATTTTCTGC
                                      | ||   |  | |  | | ||| ||   ||||  |  | | | || |||     ||| ||      |||||  |||||  ||  ||  || ||||  |||||||||| ||||||||  | |||||||||||||||||||| ||||||||||| |
gtaatcttcaagccagttttattttctttttttgcttatgtatattctctggtttgttgtaataaatctttctaaaagtgaatgcttttaataaagctgatctttttcttgtttttgaatggatattgcagGGACAAGATGTTGCCTTTGAACCTGCTAAGCTTCTGTGGCTTATCCAACGTGATTTTCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgatccatggcatccttcaaaacttcgtttctgatttttatatatcctgtagGGTGAAGATGTTGCTTTTGAACCGTCAAAGCTTCTGTGGCTTATCCAGCGTGATTTTCTGC
                               ttctgat  putative branch site (score: 3)
                              tttctgatttttatat  TA-rich tract