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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctaacatttctaagttcccggtgagagacccgcaatcaatttttccggtggaaactcattggattgataagttttattaatacagGTGGGGAGACATTGAATTTCCTCTGCCATTTGGAAGGGTCCTCAGTTCTACAGAGAACTTCATCCATGGTTTAGATGAGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G09430.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 5
gtatgtctaacatttctaagttcccggtgagagacccgcaatcaatttttccggtggaaactcattggattgataagttttattaatacagGTGGGGAGACATTGAATTTCCTCTGCCATTTGGAAGGGTCCTCAGTTCTACAGAGAACTTCATCCATGGTTTAGATGAGAAG
              ||  | ||||  | || |      ||||   || |||  ||      |  ||||||| ||   | | | |  | |||||||||||  || ||||||||||| || |||||||| || |||||  ||||||| |  ||||||||||   |||||||||||
---------gtgagtcagatttcctagggata------caat---ttcttcttgtca----ttgttggatttattcttatcaatcgtgcagGTGGGGAGGTATAGAATTTCCTCTACCTTTTGGAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAG

upper sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G340672_T01 (Zea mays), 3'ss of exon 4
gtatgtctaacatttctaagttcccggtgagagacccgcaatcaatttttccggtggaaactcattggattgataagttttattaatacagGTGGGGAGACATTGAATTTCCTCTGCCATTTGGAAGGGTCCTCAGTTCTACAGAGAACTTCATCCATGGTTTAGATGAGAAG
              ||  | |||||    |||||      | || || ||   ||      |  ||||||| |    | | | |  | |||||||||||  || ||||| ||||| || |||||||| || |||||| ||||||| |  ||||||||||   |||||||||||
---------gtgaatcagatttccc----agagat-----accatttcttgttgtca----ttgttggatttactcttatcaattgtgcagGTGGGGAGGTATAGAATTCCCTCTACCTTTTGGAAGAGTACTCAGTCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAG
















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|301502490|gb|HO208030.1|HO208030
EST:     GGAGAATTAGATGACACTGCTGCCTTCAAGAATTTCAACAA                         GTGGGGAGACATTGAATTTCCTCTGCCATTTGGAAGGGTCCTCAGTTCTAC
genomic: GGAGAATTAGATGACACTGCTGCCTTCAAGAATTTCAACAAgtatgtctaa ... attaatacagGTGGGGAGACATTGAATTTCCTCTGCCATTTGGAAGGGTCCTCAGTTCTAC
EST: gi|125106500|gb|EL159908.1|EL159908
EST:     CACTGCTGCCTTCAAGAATTTCAACAA                         GTGGGGAGACATTGAATTTCCTCTGCCATTTGGAAGGGTCCTCAGTTCTAC
genomic: CACTGCTGCCTTCAAGAATTTCAACAAgtatgtctaa ... attaatacagGTGGGGAGACATTGAATTTCCTCTGCCATTTGGAAGGGTCCTCAGTTCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcaatcaatttttccggtggaaactcattggattgataagttttattaatacagGTGGGGAGACATTGAATTTCCTCTGCCATTTGGAAGGGTCCTCAGTTCTACAGAGAACTTCATCCATGGTTTAGATGAGAAG
                                            tattaat  putative branch site (score: 2)
                                         ttttatt  CT-rich tract
                                attgataagttttatt  TA-rich tract