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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaggacgttattgtaaaacctgtttttctttgtttttttccccttgctgcgactcactagagttctattacctactaatatcttgtcaaatatgttgtatgtgaagTTCGGTTGATTTGATCATTAGTTCGTTGGGGCTTCACTGGACAAATGATCTTCCTGGATCCATGATACAG

Basic information

species Arabidopsis thaliana
transcript AT1G22800.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G22800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g10200.1 (Oryza sativa), 3'ss of exon 2
gtaacaaggacgttattgtaaaacctgtttttctttgtttttttccccttgctgcgactcactagagttctattacctactaatatcttgtcaaatatgttgtatgtgaagTTCGGTTGATTTGATCATTAGTTCGTTGGGGCTTCACTGGACAAATGATCTTCCTGGATCCATGATACAG
           |   || | | |  | |||   ||   |         || |     ||  |||      |||| |  |      | ||        | | || | ||||| |||   |||  ||| || ||||   | |||||||| |||||||||||||| |||||| | |||||||||
-----------gcagttctcacaattatttagtttaagtcaaacaatgtttcccgatcttcctatctgcatattgctcatgtcattattaatgtggttatggtctctgaagCTCGCAGGATACGATAATAAGTTGTCTTGGGCTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG

upper sequence: AT1G22800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g06830.t01 (Vitis vinifera), 3'ss of exon 4
gtaacaaggacgttattgtaaaacctgtttttctttgtttttttccccttgctgcgactcactagag--ttctattacc-tactaatatcttgtcaaatatgttgtatgtgaagTTCGGTTGATTTGATCATTAGTTCGTTGGGGCTTCACTGGACAAATGATCTTCCTGGATCCATGATACAG
           | | ||  ||  |||   |   | ||| | |     | ||     | |   | ||   || ||||  |   |||||  |||||   || |||    ||  ||||||  | ||| || | || || |  ||||| || || ||||| ||||||||||||||| |||||||||||
----------tgctctt-caatgccttcatcagtatgtatgtagattcatgtaaaaaatatgttgatgtttttattggcactctaatggcttgt---atttgtaaattgcaaagTTCTCTAGATCTGGTAATCAGCTGCTTGGGACTCCATTGGACGAATGATCTTCCTGGAGCCATGATACAG
















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|164174633|gb|ES042016.1|ES042016
EST:     GAAACCTCTTACTTTGTTGGTGATGAAGAGTTTCTGCCAGTCAAAGAGAG                         TTCGGTTGATTTGATCATTAGTTCGTTGGGGCTTCACTGGACAAA
genomic: GAAACCTCTTACTTTGTTGGTGATGAAGAGTTTCTGCCAGTCAAAGAGAGgtaacaagga ... gtatgtgaagTTCGGTTGATTTGATCATTAGTTCGTTGGGGCTTCACTGGACAAA
EST: gi|19875087|gb|AU235918.1|AU235918
EST:     AAACCCTCTTACTTTGTTGGTGATGAAGAGTTTCTGNCAGTCAAAGAGAG                         TTCGGTTGATTTGATCATTA
genomic: AAACC-TCTTACTTTGTTGGTGATGAAGAGTTTCTGCCAGTCAAAGAGAGgtaacaagga ... gtatgtgaagTTCGGTTGATTTGATCATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcactagagttctattacctactaatatcttgtcaaatatgttgtatgtgaagTTCGGTTGATTTGATCATTAGTTCGTTGGGGCTTCACTGGACAAATGATCTTCCTGGATCCATGATACAG
                     tactaat  putative branch site (score: 1)
                     tactaatat  TA-rich tract