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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccccctattcctacatttccgaatatcgtgtttccgagagaagtaagcgaaaccatattatgtaacgctacatgcacctattttccagGGCTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCATCTGTGAGATTATTTGCTGAGCGGGGAATGGAGTTTTTTGTTGCTCAGTCATATAGTAAAAATT

Basic information

species Arabidopsis thaliana
transcript AT4G31990.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 3'ss of exon 8
gtatccccctattcctacatttccgaatatcgtgtttccgagagaagtaagcgaaaccatattatgtaacgctacatgcacctattttccagGGCTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCATCTGTGAGATTATTTGCTGAGCGGGGAATGGAGTTTTTTGTTGCTCAGTCATATAGTAAAAATT
          ||     || ||    || |||| ||||   |      ||   | | | || |   || |   | ||     |  | | ||||| ||||| |||||||||||||||||||||||| | ||||| ||  | |||| | | |||||| ||||  | |||||||| ||||| ||||| |||||  
-----gtgaaatgttctcactttattatttcgtttttctctgcatgaaaacaaatatcttactgactagcaa-atat-----ttctctgcagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATCTTCTGTCAGGCTTTTTGTTCAACGGGGACTGGAAGTGTTTGTTGCGCAGTCTTATAGCAAAAACC

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 8
gtatccccctattcctacatttccgaatatcgtgtttccgagagaagtaagcgaaaccatattatgtaacgctacatgcacctattttccagGGCTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCATCTGTGAGATTATTTGCTGAGCGGGGAATGGAGTTTTTTGTTGCTCAGTCATATAGTAAAAATT
         |   | |   |    || || | ||| ||| |   | |||  || ||  || |  |  |  |     |   | |   ||  |||| ||||| ||||||||||||||||||||||||   ||||| ||  | |||| | |||| || |||||  | |||||||| || || || || || ||  
--------gtgaacgtttttgcttgagtaccttgtctcctacgtatgtat-cgcaat-atctcttccactgactggtaggctttccttttagGGTTTTGCCAGTGGAAGCCTTGATGAAGATGCATTTTCTGTCAGGCTTTTTGTTAAGCGTGGCATGGAAGTGTTTGTTGCACAATCTTACAGCAAGAACC

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 8
gtatccccctattcctacattt---ccgaatatcg--tgtttccgagagaagtaagcgaaaccatattatgtaacgctacatgcacct-att--ttccagGGCTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCATCTGTGAGATTATTTGCTGAGCGGGGAATGGAGTTTTTTGTTGCTCAGTCATATAGTAAAAATT
  || |    |    || || |   || || |     | ||         ||  | | | | | |||| || |||        | ||| |||  ||  |||| |||||||||||||||||||||||||||||||| ||||||||| | ||||  |  || || || ||| || |||| ||||| || || ||||||||| 
tgattctagaaaaattaaatctaatccaaacacacactattaatctttatagagacctagaacctattttgcaacatgctgaactcctcattaattttagGGGTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCTTCTGTGAGACTGTTTGTGGCACGTGGCATCGAGGTTCTTGTAGCTCAATCTTACAGTAAAAATC

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA14G13480.1 (Glycine max), 3'ss of exon 8
----gtatccccctattcctacatttccgaatatcgtgtttccgagaga-agtaagcgaaaccatattatgtaacgctacatgcacct-att--ttccagGGCTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCATCTGTGAGATTATTTGCTGAGCGGGGAATGGAGTTTTTTGTTGCTCAGTCATATAGTAAAAATT
     |        ||||    |      ||| |  |     |     | ||  | |   | | ||||  | |||   |    | ||| |||  ||  |||| |||||||||||||||||||||||||||||||| ||||||||| | ||||  |  || || |||||| || |||| ||||| || || ||||||||| 
tggaattggagttgattctataaaaattaaatctaatccaaacaccctatagagacctggaacctatttagcaacatgatgaactcctcattaattttagGGGTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCTTCTGTGAGACTGTTTGTGGCACGTGGCATGGAGGTTCTTGTAGCTCAATCTTACAGTAAAAATC

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 10
---------gtatccccctattcctacatttccgaatatcgtgtttccgagagaagtaagcgaaaccatattatgtaacgctacatgcacctattttccagGGCTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCATCTGTGAGATTATTTGCTGAGCGGGGAATGGAGTTTTTTGTTGCTCAGTCATATAGTAAAAATT
         | ||     |      ||||     ||||||    |  |  |         |      | |||   || |   ||    | | | |||  |||| ||||| |||||||||||||||| ||||||  |||| |||||||| |||||||  || || |||||| || | ||||| || ||||| ||||||||| 
ataaggtccgaataggtttgagttaacataattcaatatcacaatatcatgttggccttccattggaagattccatacctgaactcctaac-actttgtagGGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTTGCTGCACGTGGTATGGAGCTTCTGGTTGCCCAATCATACAGTAAAAATC

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|47828582|gb|CK118266.1|CK118266
EST:     ATGTCATTCAGGAAAAGAACCATATCCCATTTTTCGATGTTGCATACCAG                         GGCTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCATCTGTGAGATTATTT
genomic: ATGTCATTCAGGAAAAGAACCATATCCCATTTTTCGATGTTGCATACCAGgtatccccct ... tattttccagGGCTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCATCTGTGAGATTATTT
EST: gi|125038549|gb|EL110818.1|EL110818
EST:     ATGTCATTCAGGAAAAGAACCATATCCCATTTTTCGATGTTGCATACCAG                         GGCTTTGCTAGTG
genomic: ATGTCATTCAGGAAAAGAACCATATCCCATTTTTCGATGTTGCATACCAGgtatccccct ... tattttccagGGCTTTGCTAGTG
EST: gi|124934931|gb|EL011958.1|EL011958
EST:     ATGTCATTCAGGAAAAGAACCATATCCCATTTTTCGATGTTGCATACCAG                         GGCTTTGCTAGTGGAAGCCTTGA
genomic: ATGTCATTCAGGAAAAGAACCATATCCCATTTTTCGATGTTGCATACCAGgtatccccct ... tattttccagGGCTTTGCTAGTGGAAGCCTTGA
EST: gi|125002509|gb|EL074778.1|EL074778
EST:     CATATCCCTATTTTTCGATGTTGCATACCAG                         GGCTTTGCTAGTGGAAGCCT
genomic: CATATCCC-ATTTTTCGATGTTGCATACCAGgtatccccct ... tattttccagGGCTTTGCTAGTGGAAGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgagagaagtaagcgaaaccatattatgtaacgctacatgcacctattttccagGGCTTTGCTAGTGGAAGCCTTGATGAAGATGCAGCATCTGTGAGATTATTTGCTGAGCGGGGAATGGAGTTTTTTGTTGCTCAGTCATATAGTAAAAATT
                          atgtaac  putative branch site (score: 3)
                                           cctattttcc  putative PPT
                     atattatgtaa  TA-rich tract