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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattgtcttcttcatcgtgttctttctttcattctcagttggtgttcatgttttaatttttttcctttttcaagGGAACTGTTGTGGAGGGAACAATACAAAAGCTATTTGAAGGTCACCACATGAATTACATTGAGTGCATTAATGTAGATTACAAATCTACACGGAAAGAGT

Basic information

species Arabidopsis thaliana
transcript AT3G11910.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 6
gtaaattgtcttcttcatcgtgttctttctttcattctcagttggtgttcat--gttttaatttttttcctttttcaagGGAACTGTTGTGGAGGGAACAATACAAAAGCTATTTGAAGGTCACCACATGAATTACATTGAGTGCATTAATGTAGATTACAAATCTACACGGAAAGAGT
     |||     ||  |  |||| | | |   ||  | | | |   |||||   | |  |  |  |  ||   |  ||||||||  |||||| || ||||| ||| |||||||||||||||| || |||||||| ||||||||||||||||| || |||||||||||| ||||||| |
----gttggacatttatttttgttatatgtaagataataaatagtgtttcatcaatgtacaactactctctcgattcagGGAACTACTGTGGAAGGGACAATTCAACAGCTATTTGAAGGTCATCATATGAATTATATTGAGTGCATTAATGTTGACTACAAATCTACAAGGAAAGAAT

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 6
gtaaattgtcttcttcatcgtgttctttctttcattctcagttggtgttcatgttttaatttttttcctttttcaagGGAACTGTTGTGGAGGGAACAATACAAAAGCTATTTGAAGGTCACCACATGAATTACATTGAGTGCATTAATGTAGATTACAAATCTACACGGAAAGAGT
           |    ||  |        ||| ||| |  ||    | |    | |||| |||   | ||   | ||| |||||||||||| ||||||||  || |  |||||||||| |||||||| || || || |||||||||||||| ||||| |||||||   | ||||| |
----------gtgaatattataacaaacattttattatatgtctacgatttgttattaactttg--cgttgacccagGAAACTGTTGTGGAAGGAACAATTGAACAATTATTTGAAGGCCACCACATAAACTATATCGAGTGCATTAATGTTGATTATAAATCTAACAGAAAAGAAT

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 2
gtaaattgtcttcttcatcgtgttctttctttcattctcagttggtgttcatgttttaatttttttcctttttcaagGGAACTGTTGTGGAGGGAACAATACAAAAGCTATTTGAAGGTCACCACATGAATTACATTGAGTGCATTAATGTAGATTACAAATCTACACGGAAAGAGT
                || | | | | | | |  | |    | | || |  |   ||   ||| |||||      || ||||||| || |||||||| ||  ||||| |||| |||||||||||||| ||||| || ||||| || ||||| || || ||||| |   |||| ||||
--------------gtatagagctgtatatatgctgcatgttggctgctattaactttgctttcttcct------agAGAACTGTCGTAGAGGGAACGATTGAAAAGTTATTCGAAGGTCACCACATCAATTATATAGAGTGTATAAATGTTGACTATAAATCCAACAGGAAGGAGT

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 6
gtaaattgtcttcttcatcgtgttctttctttcattctcagttggtgttcatgttttaatttttttcctttttcaagGGAACTGTTGTGGAGGGAACAATACAAAAGCTATTTGAAGGTCACCACATGAATTACATTGAGTGCATTAATGTAGATTACAAATCTACACGGAAAGAGT
|| |||     |    ||  ||   | || || |  |  | ||  | || ||    ||| |||| |   |   || ||||||||||||||| ||||||||  || |  |||| ||||| |||||||| |||||||||||||||||||| || || || |||||||   | ||||| |
gtgaata----tgacaataatgaattatcatt-acaccaatttactttttat----taacttttctttctacaca-gGGAACTGTTGTGGAAGGAACAATTGAACAATTATTCGAAGGCCACCACATTAATTACATTGAGTGCATTAACGTGGACTATAAATCTAACAGAAAAGAAT

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 6
gtaaattgtcttcttcatcgtgttctttctttcattctcagttggtgttcatgttttaatttttttcctttttcaagGGAACTGTTGTGGAGGGAACAATACAAAAGCTATTTGAAGGTCACCACATGAATTACATTGAGTGCATTAATGTAGATTACAAATCTACACGGAAAGAGT
||| ||    ||   || | ||    ||     ||| |    || | |  |  |||| ||||| |     |    |||||||||| |||||||| ||||||||  || | |||||||| ||||| ||||| |||||||||||||| ||||| || |||||||||||| | || || |
gtatatgaggtttaacagc-tgcagctttcagtatttttcactgttctgaagttttttattttatattactggacagGGAACTGTAGTGGAGGGGACAATACAGCAGTTGTTTGAAGGGCACCATATGAACTACATTGAGTGCATCAATGTGGACTACAAATCTACAAGAAAGGAAT

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 6
------gtaaattgtcttcttcatcgtgttcttt-ctttcattctcagttgg--------tgttcat--gttttaatttttttcctttttca-agGGAACTGTTGTGGAGGGAACAATACAAAAGCTATTTGAAGGTCACCACATGAATTACATTGAGTGCATTAATGTAGATTACAAATCTACACGGAAAGAGT
       |||||     |   |   || ||||    |||||     || |||        |||| |   ||   |||  || |    ||| | ||||||||| ||| ||||| ||||| ||  | || || ||||| || |||||||| ||||| |||||||| ||||| ||||| ||||| |||||||||||||
gtatggataaatctctgttagctatgtcttctcggttttcaagagtagctgggtacattatgtttactggtgggaatccttctgtgcttttacagGGAACTGCTGTCGAGGGCACAATCCAGCAACTGTTCGAAGGGCATCACATGAACTACATAGAGTGCATCAATGTTGATTATAAATCAACACGGAAAGAGT

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ19227 (Selaginella moellendorffii), 3'ss of exon 6
gtaaattgtcttcttcatcgtgttctttctttcattctcagttggtgttcatgttttaatttttttcctttttcaagGGAACTGTTGTGGAGGGAACAATACAAAAGCTATTTGAAGGTCACCACATGAATTACATTGAGTGCATTAATGTAGATTACAAATCTACACGGAAAGAGT
                   |||     | | |   |   | ||       || | |||  || |   |  ||   ||||||| | ||| || ||||| || ||| |||| ||||| ||||| || ||||| ||||| || ||||| || || |||||||||||||| ||||||||||
-------------------gtgagtactttgtacgttgaacttcaaagctat-tcttatcttctactcacttctcagGGAACCGCTGTTGAAGGAACGATTCAACAGCTTTTTGAGGGTCATCATATGAACTACATCGAATGCATCAACGTCGATTACAAATCTACGCGGAAAGAGT

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|125191342|gb|EL206296.1|EL206296
EST:     TACAAGAACTCAACAGAGTTCTCTGTGAAAAGCTTGAGGACAAGATGAAG                         GGAACTGTTGTGGAGGG
genomic: TACAAGAACTCAACAGAGTTCTCTGTGAAAAGCTTGAGGACAAGATGAAGgtaaattgtc ... ctttttcaagGGAACTGTTGTGGAGGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttctttcattctcagttggtgttcatgttttaatttttttcctttttcaagGGAACTGTTGTGGAGGGAACAATACAAAAGCTATTTGAAGGTCACCACATGAATTACATTGAGTGCATTAATGTAGATTACAAATCTACACGGAAAGAGT
                               ttttaat  putative branch site (score: 3)
                         ttcatgttttaatttt  CT-rich tract
                            atgttttaattttttt  TA-rich tract