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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaatgattggttttggcttctctagcaagatcaagttataattgttattttctcaaatactccttttagaacttttgtatgatgtagcctggcagtgaagttgatgaaatgatacatgtctttttaactgcagAATAAAACAGTCTCTGTGTTTGAGACAACTATCCGAGTCCTTGGGGGGTTACTATCTGCTCATCTGATTGCAAGTGATTATGCAACG

Basic information

species Arabidopsis thaliana
transcript AT5G43710.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G020359_T02 (Zea mays), 3'ss of exon 3
gtgagtaatgattggttttggcttctctagcaagatcaagttataattgttattttctca--aatactccttttagaacttttgtatgatgtagcctggcagtgaagttgatgaaatgatacatgtctttttaactgcagAATAAAACAGTCTCTGTGTTTGAGACAACTATCCGAGTCCTTGGGGGGTTACTATCTGCTCATCTGATTGCAAGTGATTATGCAACG-------------
                           |   |   |   | || |||  |||    |  |  || ||  | |||     || | |    | ||  |||   |   | |       ||| | | |  || | ||  ||||||||||||| |||||||| ||||| || |  || ||  ||||||||||  | ||||| ||||| |||||||| ||||||||||| ||              
---------------------------tgctaccttttggctacaatgtttagcagcctattaacaccacattt-----ttctttgcagtatattctgcttgaacaatc------atgtttccttactgtgta--tgcagAATAAAACCGTCTCTGTTTTTGAAACCAACATACGTATCCTTGGGGGTCTGCTATCAGCTCACCTGATTGCCAGTGATTATGCCACTGTATGTTTGTTCT

upper sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G020359_T01 (Zea mays), 3'ss of exon 3
gtgagtaatgattggttttggcttctctagcaagatcaagttataattgttattttctca--aatactccttttagaacttttgtatgatgtagcctggcagtgaagttgatgaaatgatacatgtctttttaactgcagAATAAAACAGTCTCTGTGTTTGAGACAACTATCCGAGTCCTTGGGGGGTTACTATCTGCTCATCTGATTGCAAGTGATTATGCAACG----
                           |   |   |   | || |||  |||    |  |  || ||  | |||     || | |    | ||  |||   |   | |       ||| | | |  || | ||  ||||||||||||| |||||||| ||||| || |  || ||  ||||||||||  | ||||| ||||| |||||||| ||||||||||| ||     
---------------------------tgctaccttttggctacaatgtttagcagcctattaacaccacattt-----ttctttgcagtatattctgcttgaacaatc------atgtttccttactgtgta--tgcagAATAAAACCGTCTCTGTTTTTGAAACCAACATACGTATCCTTGGGGGTCTGCTATCAGCTCACCTGATTGCCAGTGATTATGCCACTGTAT

upper sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G173868_T02 (Zea mays), 3'ss of exon 3
gtgagtaatgattggttttggcttctctagcaagatcaagttataattgttattttctca--aatactccttttagaacttttgtatgatgtagcctggcagtgaagttgatgaaatgatacatgtctttttaactgcagAATAAAACAGTCTCTGTGTTTGAGACAACTATCCGAGTCCTTGGGGGGTTACTATCTGCTCATCTGATTGCAAGTGATTATGCAACG
                           |   |   |   | || |||  |||    |  |  || ||  | |||     || | |    | ||  |||   |   | |       ||| | | |  || | ||  ||||||||||||| |||||||| ||||| || |  || ||  ||||||||||  | ||||| ||||| |||||||| ||||||||||| || 
---------------------------tgctaccttttggctacaatgtttagcagcctattaacaccacattt-----ttctttgcagtatattctgcttgaacaatc------atgtttccttactgtgta--tgcagAATAAAACCGTCTCTGTTTTTGAAACCAACATACGTATCCTTGGGGGTCTGCTATCAGCTCACCTGATTGCCAGTGATTATGCCACT

upper sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 2
gtgagtaatgattggttttggcttctctagcaagatcaagttataattgttattttctcaaatactccttttagaacttttgtatgatgtagcctggcagtgaagttgatgaaatgatacatgtctt---tttaactgcagAATAAAACAGTCTCTGTGTTTGAGACAACTATCCGAGTCCTTGGGGGGTTACTATCTGCTCATCTGATTGCAAGTGATTATGCAACG
                                       || |  |||  ||||    |||  | |  || |     |||  | | ||    ||   ||   |  ||   | | | |||  ||   |   ||    ||||||||||||| || ||| | |||||||| |||||| | ||||| || || ||||| || |||||||| ||||| | ||||||||| |||
---------------------------------------gtgagtattagtattcgtccaaccattttttgt-----tttcat-taataattccattcat--acatttccgtatttatatttgctctgggttgctttgcagAATAAAACGGTTTCTCTCTTTGAGACTACTATCAGGGTCCTCGGAGGATTACTTTCAGCTCATCTTATTGCCACTGATTATGCTACG

upper sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtaatgattggttttggcttctctagcaagatcaagttataattgttattttct--caaatactccttttagaacttttgtatgatgtagcctggcagtgaagttgatgaaatgatacatgtctttttaactgcagAATAAAACAGTCTCTGTGTTTGAGACAACTATCCGAGTCCTTGGGGGGTTACTATCTGCTCATCTGATTGCAAGTGATTATGCAACG
                                   |  | | | |||  ||    |||  |      | ||  |     |  || |  ||  |  |    |   ||  |  |||  | ||     | | |  |  |||||||||| || || |||||||||||||| || |||||| ||||||| || ||||| |||| |||||| ||||| ||||||||||| |||
-----------------------------------tgtattgacaatcatttcaatctggctgggcttgctgctttggttactgcaaaataaacacatcaatctaaacttttgagcttat-----tgtgtccacttgcagAATAAGACGGTATCTGTGTTTGAGACTACCATCCGAATCCTTGGAGGTTTACTTTCTGGTCATCTTATTGCCAGTGATTATGCTACG

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|125210275|gb|EL225229.1|EL225229
EST:     GCTTCACTTCTTCTGTTGAATGGATTGGTAAAAATCTTCAGTTTAATATA                         AATAAAACAGTCTCTGTGTTTGAGACAA
genomic: GCTTCACTTCTTCTGTTGAATGGATTGGTAAAAATCTTCAGTTTAATATAgtgagtaatg ... ttaactgcagAATAAAACAGTCTCTGTGTTTGAGACAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatgtagcctggcagtgaagttgatgaaatgatacatgtctttttaactgcagAATAAAACAGTCTCTGTGTTTGAGACAACTATCCGAGTCCTTGGGGGGTTACTATCTGCTCATCTGATTGCAAGTGATTATGCAACG
                                           ttttaac  putative branch site (score: 2)
                                      tgtcttttt  CT-rich tract
                                        tctttttaa  TA-rich tract