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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaaagctctctctcttatgttttaagtccgtgttgttggaggagaactatgtttaggcaactaatatctttgtgtgtgttggattcagGGGTCGAAAGAGGGCATGTGTTACATACTGTATAGTTTACATACTAAGTTGCATCACCAAGCACTCTCCACAGTACAAAGTTTTGATGGTTGGCCGTATC

Basic information

species Arabidopsis thaliana
transcript AT3G49310.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 2
----gtgagaaagctctctctcttatgttttaagtccgt-gttgttggaggagaactatgtttaggcaactaatatctttgtgtgtgttggattcagGGGTCGAAAGAGGGCATGTGTTACATACTGTATAGTTTACATACTAAGTTGCATCACCAAGCACTCTCCACAGTACAAAGTTTTGATGGTTGGCCGTATC
    ||         |||   |||  |  | || || || | | | |           ||  || |      |      ||  | |   |   ||||||| || |||||||| ||||| || ||||| ||    ||||| || || |||||||||||||||||||| |||||||||||| | ||| |||| ||| ||
gtgcgttgcgccctcctccgccttgggggtgaattcagtcgatttcgttctgttttggtggatacggcgacgaggctgatggattttccgtggtcagGGGGCGGAAGAGGGCGTGTGTCACGTACTGCATCACCTACATCCTCAGCTGCATCACCAAGCACTCTCCCCAGTACAAAGTTCTTATGATTGGGCGTGTC

upper sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 2
gtgagaaagctctctctcttatgttttaagtccgtgttgttggaggagaactatgtttaggcaactaatatctttgtgtgtgttggattcagGGGTCGAAAGAGGGCATGTGTTACATACTGTATAGTTTACATACTAAGTTGCATCACCAAGCACTCTCCACAGTACAAAGTTTTGATGGTTGGCCGTATC
    | ||| | ||  | | || || |  ||   ||    |  |    || |  | |      | | ||    || | |       ||| |||||||| ||||||||||| ||||| ||||| |||  ||| ||||| || |||||||||||||| ||||| ||||||||| |||| ||| | || ||||| 
----gtaagatttccttttgattttgtttgtt--tgccagtctatattaatt--gatccattgattcatgatattttctacaccaaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTGCATCACCAAGCATTCTCCTCAGTACAAAATTTTAATGTTGGGACGTATA
















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|86074066|gb|DR369823.1|DR369823
EST:     GGTTCGTCAATGTTGTTTGGAACTATTGTTGGATCTCTGGCTGACAAACA                         GGGTCGAHVGAGGGCATGTGTTACATACTGTATAGTTTACATACTAAGTTG
genomic: GGTTCGTCAATGTTGTTTGGAACTATTGTTGGATCTCTGGCTGACAAACAgtgagaaagc ... ttggattcagGGGTCGAAAGAGGGCATGTGTTACATACTGTATAGTTTACATACTAAGTTG
EST: gi|19876532|gb|AU237363.1|AU237363
EST:     GGTTCGTCAATGTTGTTTGGAACTATTGTTGGATCTCTGGCTGACAAACA                         GGGTCGAAAGAGGGCATGTGTTACATACTGTATAGTTTACATACTAAGTTG
genomic: GGTTCGTCAATGTTGTTTGGAACTATTGTTGGATCTCTGGCTGACAAACAgtgagaaagc ... ttggattcagGGGTCGAAAGAGGGCATGTGTTACATACTGTATAGTTTACATACTAAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttggaggagaactatgtttaggcaactaatatctttgtgtgtgttggattcagGGGTCGAAAGAGGGCATGTGTTACATACTGTATAGTTTACATACTAAGTTGCATCACCAAGCACTCTCCACAGTACAAAGTTTTGATGGTTGGCCGTATC
                         aactaat  putative branch site (score: 2)
                            taatatcttt  TA-rich tract