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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatccgtttggttcaatttttttatattttaatctttccttgtcaattatcaagcctcacaagcccttggttttacacagCCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGATTCACAACTATCTGACCCGTGTGATGTACAACCGTCGCAACAAGTTTAAC

Basic information

species Arabidopsis thaliana
transcript AT1G56450.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G56450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G040164_T02 (Zea mays), 3'ss of exon 4
------------------------gtaagaatccgtttggttcaatttttttatattttaatctttccttgtcaattatca----agcctc--acaagcccttg----gttttacacagCCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGATTCACAACTATCTGACCCGTGTGATGTACAACCGTCGCAACAAGTTTAAC
                         || | |||    |  |   ||| | |         || ||||  | || | |   |    |   ||  ||| | | ||      || |   ||| |||  |||| | |||||||||||||| |||||  |||| || |||||||| |||| |||| ||||  | |||||||||||||| |||||||||||| | 
gtaagttccatcactaaggattaaatatggatcttcataat--gattgtatggggaacccatgtttctctttctaatgctacggaaatttcaaacacgtcattttcccattcttttcagTCTGTCTGATCATATGTGGGATGATGGAAACTCGCTGGGCCCCAAAGAGATCCACAGCTATTTGACAAGAGTGATGTACAACCGGCGCAACAAGTTTGAT

upper sequence: AT1G56450.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G023080_T02 (Zea mays), 3'ss of exon 3
------------------------gtaagaatccgtttggttcaatttttttatattttaatctttccttgtcaattatcaagcctca--caagcccttggttttaca--------cagCCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGATTCACAACTATCTGACCCGTGTGATGTACAACCGTCGCAACAAGTTTAAC
                         || | | |       |   ||| | |  |    | ||   || || || | |   | |    |   || | ||| ||||| |         ||| ||   |||| | |||||||||||||| || ||| |||| || |||||||| ||||  ||| ||||  | |||||||||||| | |||||||||||| | 
gtaagtttcatcactgacaagccaatatggaacttcacaat--gattatatggtgaactcatgcctctttttctaatgctaggaaaaaattaaactcttcgttttccctttcttttcagTCTTTCTGATCATATGTGGGATGATGGAAATTCTCTGGGCCCCAAAGAGATCCACAGTTATTTGACAAGAGTGATGTACAACAGACGCAACAAGTTTGAT
















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|86055052|gb|DR350809.1|DR350809
EST:     GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCAC                         CCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGAT
genomic: GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatcc ... ttttacacagCCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGAT
EST: gi|116438502|gb|EG481094.1|EG481094
EST:     GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCAC                         CCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGAT
genomic: GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatcc ... ttttacacagCCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGAT
EST: gi|125162895|gb|EL189665.1|EL189665
EST:     TCAGGAGATTCTCCGTTATCTTGATGAGCTCAC                         CCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAA
genomic: TCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatcc ... ttttacacagCCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAA
EST: gi|86055051|gb|DR350808.1|DR350808
EST:     GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCAC                         CCTGAATGNTAACATGTGGGGATGATGGT
genomic: GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatcc ... ttttacacagCCTGAATGATAACATGTGGG-ATGATGGT
EST: gi|86055050|gb|DR350807.1|DR350807
EST:     GGAGAAATCAGCGACTTTCAGGAGATTCTCCATTATCTTGATGAGCTCAC                         CCTGAATGATAACATNTGGGATGATGGTAACTCTTTGGGACCAAAAGAGAT
genomic: GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatcc ... ttttacacagCCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttaatctttccttgtcaattatcaagcctcacaagcccttggttttacacagCCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGATTCACAACTATCTGACCCGTGTGATGTACAACCGTCGCAACAAGTTTAAC
                            gcctcac  putative branch site (score: 3)
                   aattatcaa  TA-rich tract