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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACAAGGGTGGAATCTACATGGTCTTTGAGTACATGGATCATGACTTGACTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAGgtattgcatggctagacaccttgttgtagtagcctttgcaaaaacccttattgttccgactttgtctgacatttgaacatatgtaaaaaag

Basic information

species Arabidopsis thaliana
transcript AT5G64960.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G64960.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os05g32360.1 (Oryza sativa), 5'ss of exon 5
ATACAAGGGTGGAATCTACATGGTCTTTGAGTACATGGATCATGACTTGACTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAGgtattgcatggctagacaccttgttg--tagtagcctttgcaaaaacccttattgttccgactttgtc----tgac--atttgaacatatgtaaaaaag
 ||||||||  | || ||||||||||| ||||||||||| ||||||||||||||  | || ||| | |||||  || | || || || || ||||| ||||||   |    |   |     || ||  |  | |  |      |     || ||| ||| |   || |    | ||   | | | |   ||||  |   
GTACAAGGGGAGCATTTACATGGTCTTCGAGTACATGGACCATGACTTGACTGGGTTGGCAGATAGGCCTGGGATGCGTTTCACCGTGCCGCAGATTAAGgtaaaaccatccattatgttatgatggctcttggtttgctaggaggtagttcttgatccaatgatggcaagataactggtataacctcttgtaccag--

upper sequence: AT5G64960.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 5'ss of exon 5
ATACAAGGGTGGAATCTACATGGTCTTTGAGTACATGGATCATGACTTGACTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAGgta---ttgcatggctagacaccttgttgtagtagcctttgcaaaaacccttattgttcc-gact--ttgtctgacatttgaacatatgtaaaaaag-
 ||||||||  | |||||||||||||| |||||||||||||||||  | ||||| ||||| ||| | |||||  || | || || || |||||||| ||||||      | ||  |      |||||| | ||      ||  | |    || || |  | ||||  |  |||||  | ||| | | | |        
GTACAAGGGGAGCATCTACATGGTCTTCGAGTACATGGATCATGATCTTACTGGGCTTGCAGATAGGCCTGGGATGCGGTTCACTGTGCCTCAGATTAAGgtagaaccacctgtttgtgtgacttgttcttgtt-tggatgtgatatattttgttatgacagactgatcttctgatgtgtgatcttctatcgtcccag

upper sequence: AT5G64960.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv00s0805g00020.t01 (Vitis vinifera), 5'ss of exon 4
ATACAAGGGTGGAATCTACATGGTCTTTGAGTACATGGATCATGACTTGACTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAGgtattgcatggctagacaccttgttgtagtagcctttgcaaaaacccttattgttccgactttgtctgacatttgaacatatgtaaaaaag------------
|||||  ||||| ||||||||||| ||||| |||||||| ||||| ||  | || ||  ||||||||||||||||||||||| |  |||||||| | ||||| |   ||| ||| |   |||     ||||   |||  |       ||| | ||  | |  ||        ||||  || |    | ||             
ATACAGAGGTGGCATCTACATGGTTTTTGATTACATGGACCATGATTTAGCAGGCCTGTCTGATCGTCCTGGACTGAGATTTTCAATTCCTCAGGTCAAGgtgtgatatgtctataatgctt-----agtaagattttta-----ttttacttttgtggcgatgaaaattccttgatgatttaccgacaaactttcttttcag

upper sequence: AT5G64960.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S3_535V6.2 (Physcomitrella patens), 5'ss of exon 3
ATACAAGGGTGGAATCTACATGGTCTTTGAGTACATGGATCATGACTTGACTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAGgtattgcatg----------gctagacaccttgt--tgtagtagcctttgcaaaaacccttattgttccgactttgtctgac---atttgaacatatgtaaaaaag------------------------------------------------
 | ||| |||   || |||||||| || ||||||||||| |||||  ||||||| ||||| ||||| |||||| || | ||  |  |||| || || |||||| | | ||          |||     ||| ||  |||| |   |||| |   |    |  || ||||  || | |||  |    ||    | | ||    |                                                   
GTTCAAAGGTTCTATTTACATGGTGTTCGAGTACATGGACCATGATCTGACTGGTCTTGCAGATCGACCTGGAATGCGCTTCTCTATTCCCCAAATCAAGgtacttcgtgtagatgaattgcttacttcctggtgatgtatttctcttttcttcatttttccttcttcccgctctctctctctctgttctgtcttttgccttatcatttttttcgactcaatcttgaggtttaatatggtcttctataatgcag

upper sequence: AT5G64960.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S235_102V6.1 (Physcomitrella patens), 5'ss of exon 4
ATACAAGGGTGGAATCTACATGGTCTTTGAGTACATGGATCATGACTTGACTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAGgtattgcatggctagacacctt-gttgtagtagc---------ctttgcaaaaacccttattgttccgactttgtctgacat--ttgaa---catatgtaaaaaag-----------------
 | ||| ||    || |||||||| |||||||||||||| ||||| |||||||| ||||||||||| |||||  || | ||  |  |||| || || |||||| | | |||    | |||||   ||    |||         || ||       ||||| | ||| | | | || |  ||      |    ||  | | || | |                 
GTTCAAAGGCTCTATTTACATGGTGTTTGAGTACATGGACCATGATTTGACTGGCCTTGCTGATCGGCCTGGGATGCGCTTCTCTATTCCCCAAATCAAGgtacttcgtgggatcaaaccttcactgcttgagcgaattttctctctgtttccttccttacttttctgtcctcgttttgcacagcccagttccaagttttaacatggatcttcttcactgcag

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
EST: gi|47829487|gb|CK119171.1|CK119171
EST:     CTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAG                         TGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAA
genomic: CTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAGgtattgcatg ... tgtaaaaaagTGTTACATGAAGCAACTGCTGACTGGGCTTCACTATTGTCATGTGAATCAA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACAAGGGTGGAATCTACATGGTCTTTGAGTACATGGATCATGACTTGACTGGACTTGCTGATCGTCCTGGACTGAGATTTACGGTTCCTCAGATAAAGgtattgcatggctagacaccttgttgtagtagcctttgcaaaaacccttattgttccgactttgtctgacatttgaacatatgtaaaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT