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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcatggctagacaccttgttgtagtagcctttgcaaaaacccttattgttccgactttgtctgacatttgaacatatgtaaaaaagTGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAAGTGCTTCACCGTGATATAAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G64960.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G64960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g32360.1 (Oryza sativa), 3'ss of exon 5
gtattgcatggctagacaccttgttgtagtagcctttgc-------aaaaacccttattgttccgactttgtct-gacatttg----aacatatgtaaaaaagTGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAAGTGCTTCACCGTGATATAAAAG
     | |   | |  ||   |||| |  | ||  |||          |     || ||| ||| |   || |  || |  ||    ||| | | |  |  ||||||||||||||||||| || || || ||||| ||||||||  | |||||||| || || |||||||| ||||
-----gtaaaaccatccattatgttatgatggctcttggtttgctaggaggtagttcttgatccaatgatggcaagataactggtataacctct-tgtaccagTGTTACATGAAGCAACTCCTTACAGGCCTTCATTATTGTCACATTAATCAAGTTCTGCATCGTGATATTAAAG

upper sequence: AT5G64960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0141g00280.t01 (Vitis vinifera), 3'ss of exon 5
gtattgcatggctagacaccttgttgtagtagcctttgcaaaaacccttattgttccgactttgtctgacatttg--aacatatgtaaaaa--agTGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAAGTGCTTCACCGTGATATAAAAG
|| |   ||| ||| |   |||   |||  |   ||     |      |   | |   | ||  |     ||||    ||| |  |       ||||||| ||||||||  | ||||||||||||||||| ||||| || |||||||| |||||| | || || ||||
gtgtgatatgtctataatgctta--gtaagatttttattttacttttgtggcgatgaaaattccttgatgatttaccgacaaactttcttttcagTGTTATATGAAGCAGTTACTGACTGGGCTTCACTACTGTCACGTCAATCAAGTACTTCACAGGGACATCAAAG

upper sequence: AT5G64960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0805g00020.t01 (Vitis vinifera), 3'ss of exon 4
gtattgcatggctagacaccttgttgtagtagcctttgcaaaaacccttattgttccgactttgtctgacatttg--aacatatgtaaaaa--agTGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAAGTGCTTCACCGTGATATAAAAG
|| |   ||| ||| |   |||   |||  |   ||     |      |   | |   | ||  |     ||||    ||| |  |       ||||||| ||||||||  | ||||||||||||||||| ||||| || ||||||                      
gtgtgatatgtctataatgctta--gtaagatttttattttacttttgtggcgatgaaaattccttgatgatttaccgacaaactttcttttcagTGTTATATGAAGCAGTTACTGACTGGGCTTCACTACTGTCACGTCAATCAA----------------------

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|124756282|gb|EH846412.1|EH846412
EST:     CCTGGACTGAGATTTACGGTTCCTCAGANAAAG                         TGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAA
genomic: CCTGGACTGAGATTTACGGTTCCTCAGATAAAGgtattgcatg ... tgtaaaaaagTGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAA
EST: gi|164005784|gb|ES007546.1|ES007546
EST:     TGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGAATAAAG                         TGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTG
genomic: TGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGA-TAAAGgtattgcatg ... tgtaaaaaagTGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTG
EST: gi|164179696|gb|ES010118.1|ES010118
EST:     CTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAG                         TGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTG
genomic: CTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAGgtattgcatg ... tgtaaaaaagTGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTG
EST: gi|86059280|gb|DR355037.1|DR355037
EST:     CTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAG                         TGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAA
genomic: CTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAGgtattgcatg ... tgtaaaaaagTGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAA
EST: gi|86059279|gb|DR355036.1|DR355036
EST:     CTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAG                         TGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAA
genomic: CTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAGgtattgcatg ... tgtaaaaaagTGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaaaacccttattgttccgactttgtctgacatttgaacatatgtaaaaaagTGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAAGTGCTTCACCGTGATATAAAAG
                           gtctgac  putative branch site (score: 3)
                                       aacatatgtaaaaaa  TA-rich tract