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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataagcttcatctttttgacagtttaatctataacccctgcgaaaccactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCAAACATGAGCATTGTGGTAAAAGCTCTTCAACCATTGTTGAGGTCATCAA

Basic information

species Arabidopsis thaliana
transcript AT3G59350.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G59350.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 7
gtataagcttc-----atctttttgacagtttaatctataacccctgcgaaac-cactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCAAACATGAGCATTGTGGTAAAAGCTCTTCAACCATTGTTGA--GGTCATCAA
|| |     ||     ||       | | ||  |   || |  | ||  |  |   |||||       |  ||   | ||         |     | |  || | ||||| || || || ||||||||||| || ||||| ||| | |||||| | |||||||||||||||||||| || ||| |    ||| || | |   || | |  
gtctcgatctctatacatgcacacaatatttatacacatgagtcatgatagtcatcctttccttctcttttcccccacatttctcactactgcactttctcgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCAAACATGAGCATTGTGGTGAAGGCTTTATCTCCACTGCTCACAAGTAAGC--

upper sequence: AT3G59350.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os09g33860.1 (Oryza sativa), 3'ss of exon 7
---------------gtataagcttcatctttttga-cagtttaatctataacccctgcgaaaccactttcaaaacgctaaccataaaata---ctgtttcgccttgttcttgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCAAACATGAGCATTGTGGTAAAAGCTCTTCAACCATTGTTGAGGTCATCAA-
                  |   ||| |  |     | || | |  | |||   | ||| |      |   ||| |   |||||| ||  |    |   |        |   |    | |||||||| || || || ||| | ||||||||||| || || |||||||| |||| ||||||||||||||| || || ||    ||  |  |   | ||| || 
gtctgcctccctcctcccttccctttaaatgcacaagcactctcttgtatggtcactgtgtggagccaagcaacatcgtaaccaaaatttgagcccaatggtttccatctgtttattgcagCTCGCAGCGGTGGCGGCACTCTGTGTGCAATACGAGTCTGAGTTTAGACCAAGCATGAGCATTGTGGTCAAGGCACTCTCCCCTCTTCTCCAG-CATAAAC

upper sequence: AT3G59350.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G071877_T01 (Zea mays), 3'ss of exon 7
gtataagcttcatctttttg---acagtttaatctataacccctgcgaaaccactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCAAACATGAGCATTGTGGTAAAAGCTCTTCAACCATTGTTGAGGTCATCAA
||  |   || | |   | |   ||   |   |  || |    |    |   | ||    | |  | |       |  |  |||| |||||  ||  | || ||||| |||||||| |||||| ||||||||||||| ||| ||||||| ||||| |||||||||||||| || || || |||   ||  |  |      |  | 
gtcaacattttaccccctcgtacacgtctctgtgaatgatgtttttacattaatttggccatcttttattgatgtaatccctttc-ccttggactctccctgcagCTTGCTGCAGTGGCAGCACTGTGTGTGCAATACGAAGCAGAGTTCAGGCCCAACATGAGCATTGTTGTGAAGGCGCTTTCGCCTCTCCTTCAACAAAGAC

upper sequence: AT3G59350.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G346132_T01 (Zea mays), 3'ss of exon 7
-gtataagcttcatctttttgacagtttaatctataacccctgcgaaaccactttcaaaacgctaaccataaaatactgtt-tcgccttgttcttgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCAAACATGAGCATTGTGGTAAAAGCTCTTCAACCATTGTTGAGGTCATCAA
            |||  |      | |  ||   | | |   | | ||| | || | |    ||      | |||  | |  |  |  | ||  |   |  ||||| ||||| |||||||| |||||||||||||||||| | || ||                                                        
gtcccccatactatccatacatgtgctgtatgcgtgagcttggggcaactaattgctattttctctatccagaattttttaattactgtttttgtctacgccagCTTGCTGCTGTAGCAGCTTTGTGTGTGCAATATGAAGCTGAATTC-------------------------------------------------------

upper sequence: AT3G59350.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 8
----------------------------------------gtataagcttcatctttttgacagtttaatctataacccctgcg-aaaccactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCAAACATGAGCATTGTGGTAAAAGCTCTTCAACCATTGTTGAGGTCATCAA
                                          ||  |    |   | |||||  || |||  |   |   |||    | | |  ||  |  | | ||  |||   | || ||    |||  | | |     |||| || || || || ||  |||| ||||| |||||| | |||||||||||||| ||||||||||| || ||||| || |||||| |  ||| |||  |  
gtatatatttctctttctcactcctcttaattgcacaagcacatgtgaaaaagactcttgactcttgaataaagttctggtgcttggatctccatcttatggttgacattaa--caatgcttattgttggccatac-----agCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCCG

upper sequence: AT3G59350.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 8
gtataagcttcatctttttgacagtttaatctata-acccctgcgaaaccactttcaaaacgctaacca------------taaaatactgtttc------------------gccttgttcttgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCAAACATGAGCATTGTGGTAAAAGCTCTTCAACCATTGTTGAGGTCATCAA
||||    |||   || |      | | |  |  |  | | || ||||  ||| |  |  |   ||  |            |  |   |  |||                   ||||  |  |  |  | ||||| |  || || || ||| |||| ||||| |||||| | |||||||||||||| ||||||||||| || ||||| || |||||| |  ||| |||  |  
gtatctatttctatttctcactcctcttaagtgcacgcacatgtgaaaagactattgactcatgaataaagttctggtgcttggatctccattttatggttgacattaaccgtgcctactgttgaccgtgcagCTTGGAGCTGTTGCGGCACTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCTG

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|124713101|gb|EH804503.1|EH804503
EST:     GTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG                         CTCGCTGCAGTAGC
genomic: GTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagctt ... tgcgcttcagCTCGCTGCAGTAGC
EST: gi|124902181|gb|EH976261.1|EH976261
EST:     AAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG                         CTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTT
genomic: AAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagctt ... tgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTT
EST: gi|124923147|gb|EL001368.1|EL001368
EST:     CCTAAAGCTGTTGCAAAG                         CTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCA
genomic: CCTAAAGCTGTTGCAAAGgtataagctt ... tgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCA
EST: gi|86079614|gb|DR375371.1|DR375371
EST:     GTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAG                         CTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCA
genomic: GTGTTGATCCAAAACTAAAGGGAGAATATCCTCCTAAAGCTGTTGCAAAGgtataagctt ... tgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCAAACATGAGCATTGTGGTAAAAGCTCTTCAACCATTGTTGAGGTCATCAA
            cgctaac  putative branch site (score: 2)
                               tttcgccttgttctt  putative PPT
                    ataaaatactgttt  TA-rich tract