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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatagtttgttgtaaacattgatttacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAGACTTTGATTGAGGCTCATGTTGATGTTAAAACCACCGACAGTTACACTC

Basic information

species Arabidopsis thaliana
transcript AT3G04840.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g10340.1 (Oryza sativa), 3'ss of exon 3
gtaaggatagtttgttgtaaacattgatttacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgtttttt--ttaatcatctt-tagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAGACTTTGATTGAGGCTCATGTTGATGTTAAAACCACCGACAGTTACACTC
                                           |  | |||  || | |     | ||||    | |     ||   |  ||  |    | |  | || |||||||||   || || |||||||| || || ||| | |||||||||||||||||  |||||||||||||||| ||||| |||||||| ||| | ||||  |
------------------------------------------gtaattattccttcataggagaaaattacttctattagatttattttgttgctaaccagttctattgtagGGCATGTCGTTTACTACCGATAAGCTCAGATCACTTGTTAAGAAGTGGCAGACACTGATTGAGGCTCATGTGGATGTCAAAACCACAGACGGCTACATGC

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g18550.1 (Oryza sativa), 3'ss of exon 3
gtaaggatagtttgttgtaaacattgatt-tacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAGACTTTGATTGAGGCTCATGTTGATGTTAAAACCACCGACAGTTACACTC
           |     | | |||||||| | ||| | |  || ||    |||  |     | ||   || |   | || ||  | |     |   |  ||  ||| |||||||||   || ||||| || ||||||||||| ||||| ||||| ||||| || |||||||| || ||||| |||||||| ||||| || |  ||||  |
----------gtaagaatgagcattgattgttcattaatccttttg--tgttgtatctgtgatcccttttgtc-ctatgtagtctaaaccaatacat--attttctctagGGCATGAGTTTTACCACGGACAAACTTAGGTCCTTGGTCAAGAAATGGCAAACATTGATTGAAGCCCATGTGGATGTTAAGACCACAGATAACTACATGC

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G013457_T01 (Zea mays), 3'ss of exon 3
gtaaggatagtttgttgtaaacattgatttacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAGACTTTGATTGAGGCTCATGTTGATGTTAAAACCACCGACAGTTACACTC
                           |    ||||| | ||||| |  |   |       |||  | |   ||| |  | | | |||  ||||||||    |   ||||||||| | || ||||||||||| || || ||  | || |||||||||||||| |||||||| || ||||||||||| || || |||||||  ||||  |
--------------------------gtaatgatcagca-ttctgttactcactgctgttgcccttaattctgttctctatcataacttgttttttta----ttactagGGCATGAATTTTACCACCGATAAGCTCAGATCTCTAGTAAAGAAGTGGCAGACATTGATTGAAGCCCATGTTGATGTCAAGACAACCGACAACTACATGC

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0030g01810.t01 (Vitis vinifera), 3'ss of exon 4
gtaaggatagtttgttgtaaacattgatttacatcagtaattctggtcattggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAGACTTTGATTGAGGCTCATGTTGATGTTAAAACCACCGACAGTTACACTC
                ||   ||| |    |   |||| |  ||  |  ||  | |  | |  || |  | |    | | | ||     ||||||||||| || || |||| |||||||| || || || || || ||||| |||||    ||||||||||| ||||||||||||||||| |||||||| || || || |  ||||| |
----------------gtgggcatag---catgacagttagcctttttttttttaattacatgcaaaagaggaaaattggggtttctcattttttttaataat-ttcagGGAATGGACTTTACAACAGACAAGCTGAGGTCTTTGGTGCGCAAGTGGCAGACATTGATTGAGGCTCATGTGGATGTTAAGACAACAGATAACTACACCC

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S219_50V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaggatagtttgttgtaaacattgatttacatc-agtaattctggtcatt--ggttaaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAGACTTTGATTGAGGCTCATGTTGATGTTAAAACCACCGACAGTTACACTC
           |||||| ||| |   | |  | |  | ||  ||||    ||  ||   || |     ||   |  ||   ||  | ||  |||  ||   ||   || |||||||||||| |||||||||| || ||  | || || ||    |||||||||| ||||||||||||||| ||||| || || ||||| ||||  ||||   
---------tgttgttggaaaaaggaaatatcgtggaatatgtctgtatgtttcggggtaagagtgaggacagttcttaatgaa-tggatcgttcctt--gattggctctagGGCATGGACCTCACCACCGACAAGCTGCGCTCCTTAGTACGAAAGTGGCAGAGTTTGATTGAGGCTCACGTTGACGTGAAGACCACTGACAACTACATGA

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|116436618|gb|EG479210.1|EG479210
EST:     CTGTGCCAATTCTGG                         GGCATGGACTTC-CCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: CTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|125006514|gb|EL078783.1|EL078783
EST:     GCCAATTCTGG                         GGCATGGACTTCACCACCGTATAAACTTAGGTCATTGGTTAAGAAGTGGCA
genomic: GCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCG-ATAAACTTAGGTCATTGGTTAAGAAGTGGCA
EST: gi|124903164|gb|EH977244.1|EH977244
EST:     ATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: ATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|125198295|gb|EL213249.1|EL213249
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGG
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGG
EST: gi|125094796|gb|EL152170.1|EL152170
EST:     TCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTCGTGCCAATTCTGG                         GGCATGGACTTCA
genomic: TCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCT-GTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCA
EST: gi|164178285|gb|EL971970.1|EL971970
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTC
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTC
EST: gi|124738495|gb|EH829775.1|EH829775
EST:     AGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: AGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|164037895|gb|ES154790.1|ES154790
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCGATGGACTTCACCACCGATAAACTTAGGTCATTG
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGC-ATGGACTTCACCACCGATAAACTTAGGTCATTG
EST: gi|124912755|gb|EH986745.1|EH986745
EST:     ATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTAGGTTAAGAAGTGGCA
genomic: ATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATT-GGTTAAGAAGTGGCA
EST: gi|116425121|gb|EG467713.1|EG467713
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|124865708|gb|EH950145.1|EH950145
EST:     TGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCGG
genomic: TGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|116436720|gb|EG479312.1|EG479312
EST:     CTGTGCCAATTCTGG                         GGCATGGACTTC-CCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: CTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|125258688|gb|EL272773.1|EL272773
EST:     CGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: CGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|125044772|gb|EL117041.1|EL117041
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGA
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGA
EST: gi|125306848|gb|EL320933.1|EL320933
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGT
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGT
EST: gi|124887667|gb|EH966569.1|EH966569
EST:     AACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: AACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|125319767|gb|EL333852.1|EL333852
EST:     AACGCTCTGTGCCAATTCTGG                         GGCNTGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
genomic: AACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAG
EST: gi|125170110|gb|EL193765.1|EL193765
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCAC
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCAC
EST: gi|124732806|gb|EH824208.1|EH824208
EST:     AGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGT
genomic: AGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGT
EST: gi|124724280|gb|EH815682.1|EH815682
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCG
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCG
EST: gi|124966709|gb|EL040795.1|EL040795
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTAGGT
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTAGGT
EST: gi|124734648|gb|EH826050.1|EH826050
EST:     GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGG                         GGCATGGACTTCACCACCGATAAACTTA
genomic: GTCTCAGAGCTGAAGATGTCCAGGGCAGGAACGTTCTGTGCCAATTCTGGgtaaggatag ... tcatctttagGGCATGGACTTCACCACCGATAAACTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaaacccagattatggttgtggagcttgactgttttttttaatcatctttagGGCATGGACTTCACCACCGATAAACTTAGGTCATTGGTTAAGAAGTGGCAGACTTTGATTGAGGCTCATGTTGATGTTAAAACCACCGACAGTTACACTC
                                       ttttaat  putative branch site (score: 3)
                                             tcatcttt  CT-rich tract
                                 tgttttttttaatcat  TA-rich tract