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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctttttcttccttgaagttttatgttcgcacagggtttctctcatttgaactcttttttttttcctaactttattcattttgtacagTAAAAACAAATGACATGATGCTCGTAATCTACCTTTCTTCGCTTATCCGAAGTGTAATCGCCCTCCACAGTTTGATCAACAACAAG

Basic information

species Arabidopsis thaliana
transcript AT3G11270.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 5
----gtttgctttttcttccttgaagttttatgttcgcacagggtttctctcattt--gaactcttttttttttcctaactttattcattttgtacagTAAAAACAAATGACATGATGCTCGTAATCTACCTTTCTTCGCTTATCCGAAGTGTAATCGCCCTCCACAGTTTGATCAACAACAAG
      |||| | || ||   |||  |   ||  | |  | |   || ||  |||   |    | || | || ||         ||  ||||||||||| |||||||| ||||||||| | ||||| || || ||||| || ||||| ||||| || || || |||| |||||||||||| |||
gtaatcttgcatctttttttctgatttaacataattgacctgatcttttcatattctcgggagccttatgttgtc---------tttcttttgtacagTGAAAACAAACGACATGATGTTGGTAATATATCTGTCTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG

upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 8
gtttgctttttcttccttgaagttttatgttcgcacagggtttctctcatttgaactcttttttttttcctaactttattcattttgtacagTAAAAACAAATGACATGATGCTCGTAATCTACCTTTCTTCGCTTATCCGAAGTGTAATCGCCCTCCACAGTTTGATCAACAACAAG
| ||    ||| |  |||| | | ||   |    |     ||| |||    ||   ||| ||||   |  |   | | ||     |||  ||| ||||||||||| |||||||| ||||| ||||| || || || ||  |||||||||| || |||||||  ||||| |||||||| 
ggttaagatttgtgacttgtattattgaat----atcatatttttctagaatg---tctcttttaaattgttgatcttttgtacatgtgtaGTGAAAACAAATGATATGATGCTGGTAATATACCTCTCATCTCTCATTAGAAGTGTAATTGCACTCCACAACTTGATTAACAACAA-

upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 8
-----gtttgctttttcttccttgaagttttatgttcgcacagggtttctctcatttgaactcttttttttttcctaactttattcattttgtacagTAAAAACAAATGACATGATGCTCGTAATCTACCTTTCTTCGCTTATCCGAAGTGTAATCGCCCTCCACAGTTTGATCAACAACAAG
     |      | || ||   ||   |||  | |   ||    ||   ||| | ||   | |  | |||  |||     |      || | | |||| ||||||||||| |||||| | || || || ||||| || || ||||||||||| || || |||||||  |||||||| ||||||
gtgaggccaagatattattttctgcc-tttggtatcttcatcatgtca-tctaactttt-cccactctttgatccatgtgtgcccttttctatgcagTGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG

upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ21414 (Selaginella moellendorffii), 3'ss of exon 7
gtttgctttttcttccttgaagttttatgttcgcacagggtttctctcatttg----aactcttttttttttcctaactt---tattcattttgtacagTAAAAACAAATGACATGATGCTCGTAATCTACCTTTCTTCGCTTATCCGAAGTGTAATCGCCCTCCACAGTTTGATCAACAACAAG
                                    | | |||| | | ||||    || | || | | ||  ||||  |   | |  | ||| | |||| || || || |||||||||||||| ||||| || ||||| ||||||||||| || ||||| || |||| | | ||||||||||||
----------------------------------gtaagatttcacgcgtttggccaaagttttctctcttagctaagctccgtgtcaaatttttccagTCAAGACGAACGACATGATGCTCGTCATCTATCTCTCTTCTCTTATCCGAAGCGTCATCGCTCTACACAATCTCATCAACAACAAG

upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ23777 (Selaginella moellendorffii), 3'ss of exon 7
gtttgctttttcttccttgaagttttatgttcgcacagggtttctctcatttg----aactcttttttttttcctaa-ctttattcattttgtacagTAAAAACAAATGACATGATGCTCGTAATCTACCTTTCTTCGCTTATCCGAAGTGTAATCGCCCTCCACAGTTTGATCAACAACAAG
                                    | | |||| | | ||||    || | || | | ||  |||| || | | ||  || | |||| || || || |||||||||||||| ||||| || ||||| ||||||||||| || ||||| || |||| | | ||||||||||||
----------------------------------gtaagatttcacgcgtttggccaaagttttctctcttagctaagctctgtccaaattttccagTCAAGACGAACGACATGATGCTCGTCATCTATCTCTCTTCTCTTATCCGAAGCGTCATCGCTCTACACAATCTCATCAACAACAAG

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|86084913|gb|DR380672.1|DR380672
EST:     CAACTTGCTTCCTAACTTGAACGTCAACGAGTTGGTTAAAGCCTTTGCAG                         TAAAAACAAATGACATGATGCTCGTAATCTACCTTTCTTCGCTTATCCGAA
genomic: CAACTTGCTTCCTAACTTGAACGTCAACGAGTTGGTTAAAGCCTTTGCAGgtttgctttt ... ttttgtacagTAAAAACAAATGACATGATGCTCGTAATCTACCTTTCTTCGCTTATCCGAA
EST: gi|164142698|gb|ES022038.1|ES022038
EST:     GGTTAAAGCCTTTGCAG                         TAAAAACAAATGACATGATGCTCGTAATCTACCTTTCTTCGCTTATCCGAA
genomic: GGTTAAAGCCTTTGCAGgtttgctttt ... ttttgtacagTAAAAACAAATGACATGATGCTCGTAATCTACCTTTCTTCGCTTATCCGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtttctctcatttgaactcttttttttttcctaactttattcattttgtacagTAAAAACAAATGACATGATGCTCGTAATCTACCTTTCTTCGCTTATCCGAAGTGTAATCGCCCTCCACAGTTTGATCAACAACAAG
                              tcctaac  putative branch site (score: 1)
                  ctcttttttttttcct  CT-rich tract
                     ttttttttttcctaac  TA-rich tract