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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcacagaagaatctaggagagcagtaatgcatacaaatattagaccacagaagtatcttctttatgatgttactccctacgcttttatctaatcttacagcttctacactgcagGGTTCATTGCAATGTATGCTACTCTGGCTAGCCGAGATGTTGACTGCTGTCTGATTCCCGAGTCACCCTTTTACCTTGAAGGCAAAGGAGGGCTCTATGA

Basic information

species Arabidopsis thaliana
transcript AT4G32840.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 9
gtaagttcacagaagaatctaggagagcagtaatgcatac--aaatattagaccacagaagtatcttctttatgatgttactccctacgcttttatctaatcttacagcttctacactgcagGGTTCATTGCAATGTATGCTACTCTGGCTAGCCGAGATGTTGACTGCTGTCTGATTCCCGAGTCACCCTTTTACCTTGAAGGCAAAGGAGGGCTCTATGA
                           | ||| | ||  |   |||  | ||  ||     |||||  | | |  | |   |  |      ||   || |   |      |  |   |||||||||||||||||||||||||||||| || || ||||||||                                                            
----------------------tttttctgtatttcaagcttgaatgcttgattactctgctatctgttctctagtatgtatttcagtctattgcccttaaactgttatattcatcttgcagGGTTCATTGCAATGTATGCTACTCTTGCAAGTCGAGATGTG-----------------------------------------------------------

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 7
gtaagttcacagaagaatctaggagagcagtaatgcatacaaatattag-accacagaagtatcttctttatgatgttactccctacgcttttatctaatcttacagcttctacactgcagGGTTCATTGCAATGTATGCTACTCTGGCTAGCCGAGATGTTGACTGCTGTCTGATTCCCGAGTCACCCTTTTACCTTGAAGGCAAAGGAGGGCTCTATGA
                          | |   |  |   | ||||| |  |  |   | | |  | |      || ||   ||  |   |  ||   |   ||| |  ||     || |||||||||| ||||||||||||||||||||||| || |||||                                                            
--------------------------gtatgtac-ctccccaatatgattatgatttatgaacttgcccccacatattctaccagaaagtactaaggagctttaaaatttac-tgctacagGGTTCATCGCAATGTATGCTACTCTGGCTAGTCGCGATGTG-----------------------------------------------------------

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 9
gtaagttcacagaagaatctaggagagcagtaatgcatacaaatattagaccacagaagtatcttctttatgatgttactccctacgcttttatctaatcttacagcttctacactgcagGGTTCATTGCAATGTATGCTACTCTGGCTAGCCGAGATGTTGACTGCTGTCTGATTCCCGAGTCACCCTTTTACCTTGAAGGCAAAGGAGGGCTCTATGA
                ||  |  | |    | |||   |   ||  |  |   |  |  | | |  |||| | | || |    |||  |  |   |  | ||  |  |  |||  ||||||||| |||||||||||||||||||| || ||| |||| ||                                                            
----------------attcac-atattcctcatgtgaatccatgatgaatttctaacttttttgtttta-gttatttcattatactgtccttattccttttcta--tggtaccttgcagGGTTTATTGCAATGTATGCTACTCTTGCAAGCAGAGACGTG-----------------------------------------------------------

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 9
gtaagttcacagaagaatctaggagagcagtaatgcatacaaatattagaccacagaagtatcttctttatgatgttactccctacgcttttatctaatcttacagcttctacactgcagGGTTCATTGCAATGTATGCTACTCTGGCTAGCCGAGATGTTGACTGCTGTCTGATTCCCGAGTCACCCTTTTACCTTGAAGGCAAAGGAGGGCTCTATGA
                |  |   | ||||    |  || |     | ||| || ||||   |||| |||    ||||     |  |  | ||  ||   |   |   |     | || |||||||||||| |||||||||||||| ||||| ||||||||                                                            
----------------agttcacatagcacatttctattctcgattcagagcaaagaaccttctttttt----tgtttgcttcagccatcttgactttaccagcttatctactattgtagGGTTCATTGCGATGTATGCTACTCTTGCTAGTCGAGATGTG-----------------------------------------------------------

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 8
gtaagttcacagaagaatctaggagagcagtaa-tgcatacaaatattagaccacagaagtatcttctttatgatgttactccctacgcttttatctaatcttacagcttctac-actgcagGGTTCATTGCAATGTATGCTACTCTGGCTAGCCGAGATGTTGACTGCTGTCTGATTCCCGAGTCACCCTTTTACCTTGAAGGCAAAGGAGGGCTCTATGA
                       | |   |||| || ||   |   |   |   ||  |||  ||| || | ||| |   ||  |    |||  | |  | | |    | |||  |||||||| || |||||||||||||| ||||| |||||| ||||||| ||||| ||  ||||||| ||||||||||| ||||||||||| || || || || | |||
---------------------taacaattgtaagtgtattttatcgtctaagtgcaccagttgctt-ttgaggatctggatctttttcttttcctgtgttatgatgaatactatgactgcagGTTTTATTGCAATGTATGCCACTCTTGCTAGCAGAGATGTGGACTGTTGCTTGATTCCAGAGTCACCCTTCTACCTTGAAGGAAAGGGTGGACTTTTTGA

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 9
gtaagttcacagaagaatctaggagagcagtaa-tgcatacaaatattagaccacagaagtatcttctttatgatgttactccctacgcttttatctaatcttacagcttctac----actgcagGGTTCATTGCAATGTATGCTACTCTGGCTAGCCGAGATGTTGACTGCTGTCTGATTCCCGAGTCACCCTTTTACCTTGAAGGCAAAGGAGGGCTCTATGA
                         |   |||| || ||   |   |   |   ||  |||  ||| || | ||| |   ||  |    |||  |    | |||       |||    |||||||| || |||||||||||||| ||||| |||||| |||| || ||||| ||  ||||||| ||||| ||||| ||||||||||| || || || || | |||
------------------------caattgtaagtgtattttatcctctaagtgcaccagttgctt-ttgaggatctggatctttttcttttctttctgtgttatgatgaatactatgactgcagGTTTTATTGCAATGTATGCCACTCTTGCTAGCAGAGACGTGGACTGTTGCTTGATTCCAGAGTCGCCCTTCTACCTTGAAGGAAAGGGTGGACTTTTTGA

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------gtaagttcacagaagaatctaggagagcagtaatgcatacaaatattagacc----acagaagtatcttctttatgatgttactccctacgcttttatctaatcttacagcttctacactgcagGGTTCATTGCAATGTATGCTACTCTGGCTAGCCGAGATGTTGACTGCTGTCTGATTCCCGAGTCACCCTTTTACCTTGAAGGCAAAGGAGGGCTCTATGA
                                     |||        ||   | || | ||   |     | |  || |||| ||          |||  |||||    | || ||  |  | |   |||  |  ||  |    |  | |    |||||| |||||||| ||||||||||| || || || |||||||| ||||| ||| ||||||| |||||||| || || |||||||| ||||| || || | |||
gtaacttttacatttatatttgatattcagatttacttaaaagtttttaactgtgtaagtgaagtgaggaacgttgaattattggatttgttgtgcaagcctcttccaagtaatcttgatttccaatttttcctacaaagtatttggatttgatgtgcagGATTCATTGCGATGTATGCTACACTTGCCAGTCGAGATGTAGACTGTTGTTTGATTCCAGAGTCACCATTCTATCTTGAAGGGAAAGGTGGACTTTTTGA

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|164114327|gb|ES061723.1|ES061723
EST:     CAGTGTGGAAAACGGCATTGGAATTGTCAAGCTAATGGGTCGGTACAGTG                         GGTTCATTGCAATGTATG
genomic: CAGTGTGGAAAACGGCATTGGAATTGTCAAGCTAATGGGTCGGTACAGTGgtaagttcac ... tacactgcagGGTTCATTGCAATGTATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttatgatgttactccctacgcttttatctaatcttacagcttctacactgcagGGTTCATTGCAATGTATGCTACTCTGGCTAGCCGAGATGTTGACTGCTGTCTGATTCCCGAGTCACCCTTTTACCTTGAAGGCAAAGGAGGGCTCTATGA
                                atcttac  putative branch site (score: 3)
                                         cttctac  putative PPT
                       ttttatctaatctta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcacagaagaatctaggagagcagtaatgcatacaaatattagaccacagaagtatcttctttatgatgttactccctacgcttttatctaatcttacagcttctacactgcagGGTTCATTGCAATGTATGCTACTCTGGCTAGCCGAGATGTTGACTGCTGTCTGATTCCCGAGTCACCCTTTTACCTTGAAGGCAAAGGAGGGCTCTATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG