Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtatattttgtcttttggttcatttgcaactattattttatgaatctcatgttctgactcatatacagtccttgtatctgaaaagtaatttctttttttattgctaatagtttggcatttttgctttgaatcggcagcttcaggtgtctaagtcttgttattcttatgttttggttttgatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG

Basic information

species Arabidopsis thaliana
transcript AT4G39460.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
gtttgtgtatattttgtcttttggttcatttgcaactattattttatgaatctcatgttctgactcatatacagtccttgtatctgaaaagtaatttctttttttattgctaatagtttggcatttttgctttgaatcggcagcttcag-gtgtctaagtcttgttattcttatgttttggttttgatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG
                                                                                             | |||| | || |  ||   | | ||   |||| || | |  |  |   ||||    ||   || | ||  ||    | | ||     ||   ||  | ||||||||    | || |||||  | ||||| ||||| ||||||||||||||||| || |||||||| || ||||| || ||||||    
-------------------------------------------------------------------------------------------agagttctctattca--gcagttggatttagatttatggtatacaatgtaggcttggttgtccttatgcctcatttgcttgacgtgccttttacaat--tccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG----

upper sequence: AT4G39460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G31870.1 (Glycine max), 3'ss of exon 3
gtttgtgtatattttgtcttttggttcatttgcaactattattttatgaatctcatgttctgactcatatacagtccttgtatctgaaaagtaatttctttttttattgctaa-tagtttggcatttttgctttgaatcggcagcttcaggtgtctaagtcttgttattcttatgttttggttttgatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG
                                                                                        || || | | ||   || ||||||| | | |   || |  |   |  | | |   | || |    |   | |    |  |||| |||   | | |   ||  |||||||||  |||| ||||||||||||||||||||||| ||||||||||||||||||||||| || || || || ||  | || |||    
----------------------------------------------------------------------------------------aaatagtattttacctttttgctaagttggtaaacaatactatat--acttgatgggttta----ttacatttcaatctttctgatgagctagatgaaatt-tgcagAGGGCGTTATTGCAGGAGGTACAGCTGGAGTTGTTGTTGAAACAGCTTTATACCCAATCGACACAATAAAAACACGTCTGCAG----

upper sequence: AT4G39460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G15150.1 (Glycine max), 3'ss of exon 2
gtttgtgtatattttgtcttttggttcatttgcaactattattttatgaatctcatgttctgactcatatacagtccttgtatctgaaaagtaatttctttttttattgctaatagtttggcatttttgctttgaa-tcggcagcttcaggtgtctaagtcttgttattcttatgttttggttttgatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG
                                                                                         | || | | || | || |||||||  |||         | || |  | | |   | ||    | |   | |    || |||| |||   | | |   ||  |||||||||  |||| ||||| ||||||||||||||||| |||||||||||||||||||||||||| || || || ||  | || |||    
-----------------------------------------------------------------------------------------aatagtattttatcttcttgctaa--gttcatagacaatactatatacttgatggattt---tattacatttcaatttttctgatgagctagatggaatt-tgcagAGGGCGTTATTGCAGGTGGTACAGCTGGAGTTGTTGTTGAAACAGCTTTATACCCAATTGACACAATAAAAACACGTCTGCAG----

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|86037549|gb|DR333304.1|DR333304
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037542|gb|DR333297.1|DR333297
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037537|gb|DR333292.1|DR333292
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037552|gb|DR333307.1|DR333307
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGAGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037535|gb|DR333290.1|DR333290
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|152038462|gb|AV823633.2|AV823633
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037532|gb|DR333287.1|DR333287
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGAGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037548|gb|DR333303.1|DR333303
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037533|gb|DR333288.1|DR333288
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTATAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037553|gb|DR333308.1|DR333308
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|125251215|gb|EL265300.1|EL265300
EST:     GTTAATACACAAGAAGAATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTTA
genomic: GTTAATACACAAGAAG-ATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTT-A
EST: gi|86037534|gb|DR333289.1|DR333289
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037555|gb|DR333310.1|DR333310
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037540|gb|DR333295.1|DR333295
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037541|gb|DR333296.1|DR333296
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037539|gb|DR333294.1|DR333294
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037546|gb|DR333301.1|DR333301
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         G
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcag-
EST: gi|86037546|gb|DR333301.1|DR333301
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         G
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcag-
EST: gi|86037536|gb|DR333291.1|DR333291
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTATAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037551|gb|DR333306.1|DR333306
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTATAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|152033833|gb|BP817226.2|BP817226
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037554|gb|DR333309.1|DR333309
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
EST: gi|86037544|gb|DR333299.1|DR333299
EST:     TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTG                         AGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT
genomic: TGTTAATACACAAGAAGATAAACCCTTTGATTTCTTCCGCACTCTCTTTGgtttgtgtat ... gatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagcttcaggtgtctaagtcttgttattcttatgttttggttttgatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG
                                         ttttgat  putative branch site (score: 4)
                        ttattcttatgtttt  TA-rich tract