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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttttggtttgggcctccttttcctattttaaccattgtgctttgtttctaaacgtacgagcccccccttctaaacatcatatatctcttgcaaccatgcagGTTCCGTTTGCAGCTGGTAGGGATCTAAGGCCAGGTCAACTAGGGAATATGTTACACACATTGTCCAACTG

Basic information

species Arabidopsis thaliana
transcript AT1G02090.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G02090.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G25690.1 (Glycine max), 3'ss of exon 5
gtgtgttttggtttgg-gcctccttttcctat-tttaaccat---tgtgctttgtttctaaacgtacgagcccccccttctaa-acatcatatatctcttgcaacca--tgcagGTTCCGTTTGCAGCTGGTAGGGATCTAAGGCCAGGTCAACTAGGGAATATGTTACACACATTGTCCAACTG
    ||  | | |      |  || ||  ||| |||||  ||   | ||     |||||| |  | |          |  ||  |  | |  |     |||  |     | ||||| |  |||||||||||||||||  | ||||| | |||||||||||||||| |||| ||  | || |||||
----gtcctagctcattatcatctgttattatatttaattatgtttttgacccatttctatattttcatttaatgagtagtagtagtttacctgatctttgagagtgatttcagGTCCAATTTGCAGCTGGTAGGGACTTGAGGCCTGATCAACTAGGGAATATGATACAGACTCTCTCTAACTG
















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|301502449|gb|HO207989.1|HO207989
EST:     GGTATAGTTAGGGGAAAACTGGATCAGTTAAAAAGATGTTTTGAG                         GTTCCGTTTGCAGCT
genomic: GGTATAGTTAGGGGAAAACTGGATCAGTTAAAAAGATGTTTTGAGgtgtgttttg ... aaccatgcagGTTCCGTTTGCAGCT
EST: gi|164006620|gb|EL970637.1|EL970637
EST:     AAAAGATGTTTTGAG                         GTTCCGTTTGCAGCTGGTAGGGATCTAAGGCCAGGTCAACTAGGGAATATG
genomic: AAAAGATGTTTTGAGgtgtgttttg ... aaccatgcagGTTCCGTTTGCAGCTGGTAGGGATCTAAGGCCAGGTCAACTAGGGAATATG
EST: gi|164015102|gb|ES097755.1|ES097755
EST:     GGTATAGTTAGGGGAAAACTGGATCAGTTAAAAAGATGTTTTGAG                         GTTCCGTTTGCAGCTGGTAGGGATCTAAGGCCAGGTCAAC
genomic: GGTATAGTTAGGGGAAAACTGGATCAGTTAAAAAGATGTTTTGAGgtgtgttttg ... aaccatgcagGTTCCGTTTGCAGCTGGTAGGGATCTAAGGCCAGGTCAAC
EST: gi|164205748|gb|ES045915.1|ES045915
EST:     AAAAAGATGTTTTGAG                         GTTCCGTTTGCAGCTGGTAGGGATCTAAGGCCAGGTCAACTAGGGAATATG
genomic: AAAAAGATGTTTTGAGgtgtgttttg ... aaccatgcagGTTCCGTTTGCAGCTGGTAGGGATCTAAGGCCAGGTCAACTAGGGAATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaaacgtacgagcccccccttctaaacatcatatatctcttgcaaccatgcagGTTCCGTTTGCAGCTGGTAGGGATCTAAGGCCAGGTCAACTAGGGAATATGTTACACACATTGTCCAACTG
                     ttctaaa  putative branch site (score: 2)
                        taaacatcatatat  TA-rich tract