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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttgttagtgccatgtaaacaaagagcattagtggaaagctaattttacatttgtgagagttttcttggtttttggataacagAGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACCTTTCAGTAGAA

Basic information

species Arabidopsis thaliana
transcript AT4G10000.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G10000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G086971_T04 (Zea mays), 3'ss of exon 3
gtatgt-tttgttagtgccatgtaaacaaagagcat-tagtggaaagctaat--tttacatttgtgagagtt----------ttcttggtttttggataacagAGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACCTTTCAGTAGAA
|||||  |||| ||   | ||  |  |      | | | || | | |||  |  ||    ||| ||  |  |          | ||| ||| |||    | ||||||||||||||| ||| ||||||| ||||| |||||||| ||||| |||||||| | ||| 
gtatgagtttggtaaaacaataaattctgtttacctatggtcgtaggctgctgcttctggtttctgcaatatactgattgaatcctttgttattgttccaaagAGGCATGTCCCTTCTGTAGGAGAGTTCGGGAGGCCATGACCGAGCTTGACCTTTCTGCAGAG

upper sequence: AT4G10000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G086971_T03 (Zea mays), 3'ss of exon 3
--------gtatgttttgttagtgccatgtaaacaaagagcattagtggaaagctaattttacatttgtgagagttttcttggtttttggataacagAGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACCTTTCAGTAGAA--------------------------------------
         ||  || ||||  | || | |   |  ||     |  |     | |  |   | ||   |||  |  | ||| ||| |||    | ||||||||||||||| ||| ||||||| ||||| |||||||| ||||| |||||||| | |||                                       
gtaaaacaataaattctgtt--tacc-tatggtcgtaggctgctgcttctg-gtttctgcaatatac-tgattgaatcctttgttattgttccaaagAGGCATGTCCCTTCTGTAGGAGAGTTCGGGAGGCCATGACCGAGCTTGACCTTTCTGCAGAGGTGCTCAACCTTGTCTTACATTGTTCCTTCATTTCTGC

upper sequence: AT4G10000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G086971_T02 (Zea mays), 3'ss of exon 3
--------gtatgttttgttagtgccatgtaaacaaagagcattagtggaaagctaattttacatttgtgagagttttcttggtttttggataacagAGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACCTTTCAGTAGAA
         ||  || ||||  | || | |   |  ||     |  |     | |  |   | ||   |||  |  | ||| ||| |||    | ||||||||||||||| ||| ||||||| ||||| |||||||| ||||| |||||||| | ||| 
gtaaaacaataaattctgtt--tacc-tatggtcgtaggctgctgcttctg-gtttctgcaatatac-tgattgaatcctttgttattgttccaaagAGGCATGTCCCTTCTGTAGGAGAGTTCGGGAGGCCATGACCGAGCTTGACCTTTCTGCAGAG

upper sequence: AT4G10000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G43520.2 (Glycine max), 3'ss of exon 3
----------gtatgttttgttagtgccatgtaaacaaagagcattagtggaaagc-taattttacatttgtgagagttttcttggtttttggataacagAGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACCTTTCAGTAGAA
           |    | |   |      |||||    |    || | || |     | ||| | |  |  | |   |||      || ||    |||||||||||| ||||||||| | || || ||||||||  ||||||| ||||| ||||| ||||| 
ttttttggtcttgacctctcacatatttctgtaattttattttatcattgaattttgtgattgtcccatcataaatctttcaagcattatttttcaacagAGGCATGCCCCTTTTGTAGAAGGGTCCGGGAAGCTTTGACTGAACTAGATCTTTCTGTAGAG

upper sequence: AT4G10000.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g06900.t01 (Vitis vinifera), 3'ss of exon 3
--------gtatgttttgttagtgccatgtaaacaaagagcattagtggaaagctaattttacatttgtgagagtt---ttcttggtttttggataacagAGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACCTTTCAGTAGAA
          |   ||      | | ||  |   |   |   ||| |  | ||     ||   | || |  |||||   |  ||  ||  |||  |||||||||||| ||||||||  ||||||| || || ||||| |||||||| || ||||| ||||| 
tttctactaaactcttgcaccattcaatacagctactcattgttattacatagagggattgctacttttctgagttagatgttttattgctggtcaacagAGGCATGCCCCTTTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAG

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|86045281|gb|DR341036.1|DR341036
EST:     CCAGGATGTCTCTTCTAATCCGCCTTTGCGATTGCAGCTTTTTGAATTTG                         AGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACC
genomic: CCAGGATGTCTCTTCTAATCCGCCTTTGCGATTGCAGCTTTTTGAATTTGgtatgttttg ... tggataacagAGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACC
EST: gi|86045280|gb|DR341035.1|DR341035
EST:     CCAGGATGTCTCTTCTAATCCGCCTTTGCGATTGCAGCTTTTTGAATTTG                         AGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACC
genomic: CCAGGATGTCTCTTCTAATCCGCCTTTGCGATTGCAGCTTTTTGAATTTGgtatgttttg ... tggataacagAGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACC
EST: gi|86045286|gb|DR341041.1|DR341041
EST:     CCAGGATGTCTCTTCTAATCCGCCTTTGCGATTGCAGCTTTTTGAATTTG                         AGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACC
genomic: CCAGGATGTCTCTTCTAATCCGCCTTTGCGATTGCAGCTTTTTGAATTTGgtatgttttg ... tggataacagAGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtggaaagctaattttacatttgtgagagttttcttggtttttggataacagAGGCATGTCCCTTTTGTCGGAGAGTGCGGGAAGCCATGACTGAGCTAGACCTTTCAGTAGAA
         agctaat  putative branch site (score: 3)
                                ttttcttggttttt  putative PPT
            taattttacatttgt  TA-rich tract