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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcaaaatgacatcttaaaggttgaatggaattcaatttgtctcttcttggacatttaataaagagttattttgttctaacagGGACATCAAAGGAGCAAATATATTAGTGGATCCGAATGGTGAAATCAAGTTGGCAGACTTTGGGATGGCCAAACAT

Basic information

species Arabidopsis thaliana
transcript AT1G53570.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G53570.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G140726_T01 (Zea mays), 3'ss of exon 5
---------gtattcaaaa-tgacatcttaaaggttgaatggaattcaatttgtctcttcttggacatttaataaagagttattttgttctaacagGGACATCAAAGGAGCAAATATATTAGTGGATCCGAATGGTGAAATCAAGTTGGCAGACTTTGGGATGGCCAAACAT
          | |  |||| || | ||| |     |   |  | |   || |  | |    || |    |||| | |   || ||| || |  ||| || |||||||||||||| ||| | |||| ||| ||||||||| ||||| |||| |||||||| ||||| || |||
gttgttttgttgtctaaaactgtcttctcattccataggtatagtc--atatagcacagaatgcaa---taatcatgtcatacttttttttggcagAGATATCAAAGGAGCAAACATACTCGTGGGTCCTAATGGTGAAGTCAAGCTGGCTGACTTTGGCATGGCTAAGCAT

upper sequence: AT1G53570.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G39110.1 (Glycine max), 3'ss of exon 5
gtattcaaaatgacatcttaaaggttgaatggaattcaatttgtct-cttcttggacatttaataaagagtta------ttttgttctaacagGGACATCAAAGGAGCAAATATATTAGTGGATCCGAATGGTGAAATCAAGTTGGCAGACTTTGGGATGGCCAAACAT
||| |  |||| |   || ||   ||   |  ||  | |  ||  | | |||||    |||| || ||  ||       |||| || | ||||||| |||||||| || || ||| |||| ||||| ||||||||||||||| ||||||||||||| ||||| ||||||
gtaatttaaataattactcaagatttatttataacactaaatgcatgcatcttgactctttattatagtattgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT

upper sequence: AT1G53570.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G15870.1 (Glycine max), 3'ss of exon 6
gtattcaaaatgacatcttaaaggttgaatggaattcaatttgtctcttcttggacatttaataaagagtta------ttttgttctaacagGGACATCAAAGGAGCAAATATATTAGTGGATCCGAATGGTGAAATCAAGTTGGCAGACTTTGGGATGGCCAAACAT
||| |  ||||| |  || || | || | |    || |||      | |||||    |||| || ||  ||       |||| || | ||||||| |||||||| || || ||| |||| ||||| ||||||||||||||| ||||||||||||| ||||| ||||||
gtaatttaaatggctactcaa-gatttatttatgttaaatgcaag-catcttgactctttattatagtattgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT

upper sequence: AT1G53570.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G16670.2 (Glycine max), 3'ss of exon 5
gtattcaaa--atgacatcttaaaggttga-atggaattcaa-tttgtctcttcttggacatttaataaagagttattttgttctaacagGGACATCAAAGGAGCAAATATATTAGTGGATCCGAATGGTGAAATCAAGTTGGCAGACTTTGGGATGGCCAAACAT
|||||   |  ||  |  |  ||   || | ||| |||| |   || | | ||||    ||| |  | |   ||  |||| || |  |||||| || ||||| || || ||| |||| ||||| ||||||||||||||  ||||||||||||| ||||| ||||||
gtattttgattattcctacgcaatctttaacatgaaatttaggcttatttattctctttcatattgttatc-gtggttttcttttggcagGGATATTAAAGGGGCGAACATACTAGTTGATCCTAATGGTGAAATCAAACTGGCAGACTTTGGAATGGCTAAACAT

upper sequence: AT1G53570.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 5
gtattcaaa--atgacatcttaaaggttga-atggaattcaat-ttgtctcttcttggacatttaataaagagttattttgttctaacagGGACATCAAAGGAGCAAATATATTAGTGGATCCGAATGGTGAAATCAAGTTGGCAGACTTTGGGATGGCCAAACAT
|||||   |  ||  |  |  ||   || |  ||| ||| | | || | | |||||  | |||      |  ||  |||| || |  |||||| || ||||| || || ||| |||| ||||| ||||||||||||||  ||||||||||||| ||||| ||||||
gtattttgattattcctacgcaatctttaacgtggcatttagtcttatttattctttcatattgtc---atcgtggttttcttttggcagGGATATTAAAGGGGCGAACATACTAGTTGATCCTAATGGTGAAATCAAACTGGCAGACTTTGGAATGGCTAAACAT

upper sequence: AT1G53570.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 5
gtattcaaaatgacatcttaaaggttgaatggaatt--caatttgtctcttcttggacatttaataaagagttattttgttctaacagGGACATCAAAGGAGCAAATATATTAGTGGATCCGAATGGTGAAATCAAGTTGGCAGACTTTGGGATGGCCAAACAT
||| |          | | |    ||| |||  |||    |||  |||  | |  | ||  | | | | |  |||||| |  |  |||||| |||||||| ||||| ||||||||||  || ||||| || ||||||||||| || ||||| ||||| ||||||
gtactgggttgtggttatgattacttgtatgagattgctgattcctcttatttctggcaactcagataaatatattttttcatggcagGGATATCAAAGGGGCAAACATATTAGTGGGACCTAATGGGGAGATCAAGTTGGCTGATTTTGGCATGGCAAAACAT

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|47831576|gb|CK121260.1|CK121260
EST:     CAGATTCTTGCTGGGCTTGCCTATTTACATGGACGAAATACAGTACATAG                         GGACATCAAAGGAGCAAATATATTAGTGGATCCGAATGGTGAAATCAAGTT
genomic: CAGATTCTTGCTGGGCTTGCCTATTTACATGGACGAAATACAGTACATAGgtattcaaaa ... gttctaacagGGACATCAAAGGAGCAAATATATTAGTGGATCCGAATGGTGAAATCAAGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattcaatttgtctcttcttggacatttaataaagagttattttgttctaacagGGACATCAAAGGAGCAAATATATTAGTGGATCCGAATGGTGAAATCAAGTTGGCAGACTTTGGGATGGCCAAACAT
                         atttaat  putative branch site (score: 4)
                                         ttttgttct  putative PPT
                         atttaataaagagtta  TA-rich tract