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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctcttgattctaatcctctttagttaggaatatcttttgctgtactgagcttctgctactgctttgcttttcccaccgccacctgtcaatgctgacctagcactcttttagtttctcctttatatcaggactctctggaactagcttgttcaactcaattagtctgatggcctataatgttttctatacaagTCTTCCTGTGACGACTATAATTTTTGACAAGGATATCTCTGAGGAAACAGTACTGCAATATCCCCAGATTTTACTCTATTCTCAGTCTGGAAG

Basic information

species Oryza sativa
transcript LOC_Os04g28460.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g28460.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G037335_T01 (Zea mays), 3'ss of exon 7
gtgagtctcttgattctaatcctctt-tagttaggaatatcttttgctgtactgagcttctgctact----gctttgcttttcccaccgccacctgtcaatgctgacct-agcactcttttagtttctcctttatatcaggactctctggaactagcttgttcaactcaattagtctgatggcctataatgttttctatacaagTCTTCCTGTGACGACTATAATTTTTGACAAGGATATCTCTGAGGAAACAGTACTGCAATATCCCCAGATTTTACTCTATTCTCAGTCTGGAAG
|||||| |     || |||| ||  |    || |    || |||   |  |   ||||| |||||||     |||||   |       |     ||  | |||| || | ||  | ||||||| ||  ||||| | || || || ||||| |||||||| ||||||||||||||  ||||||| ||||| ||||||||||||||| | || || | |||||||                                                                          
gtgagttttcc--ttgtaatgcttatgccattggctgcatttttcattaca---agcttatgctactttgcactttggcatgggttttgtggg-tgcaactgctcacttgagtccccttttagGTTTGCCTTTTTGTCGGGGCTATCTGGGACTAGCTTATTCAACTCAATTAGCTTGATGGCTTATAACGTTTTCTATACAAGTTTACCCGTCATGACTATA--------------------------------------------------------------------------

upper sequence: LOC_Os04g28460.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 21
gtgagtctcttgattctaatcctctttagttaggaatatcttt-tgctgtactgagcttctgctactgctttgcttttcccaccgccacctgtcaa--tgctgacctagcactcttttagtttctcctttatatcaggactctctggaactagcttgttcaactcaattagtctgatggcctataatgttttctatacaagTCTTCCTGTGACGACTATAATTTTTGACAAGGATATCTCTGAGGAAACAGTACTGCAATATCCCCAGATTTTACTCTATTCTCAGTCTGGAAG
                  ||  |   |  ||| |||| |  |  ||||  | || || ||   |     | |     ||    |   |  | ||||  | ||||   |   |  ||| ||||| || ||||| |||||  |||||||||||||| | ||||| ||  ||||  ||||||| ||||||||||||||||| ||| |||||||      ||                                                                            
------------------attgttaatgattatgaatgttctaatgctaga-tgggcatccaatttctttatatagatctattctaaatttttcaaggtactgatg-attgcattttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTTAGT--------------------------------------------------------------------------

upper sequence: LOC_Os04g28460.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 21
gtgagtctcttgattctaatcctctttagttaggaatatcttt-tgctgtactgagcttctgctactgctttgcttttcccaccgccacctgtcaa--tgctgacctagcactcttttagtttctcctttatatcaggactctctggaactagcttgttcaactcaattagtctgatggcctataatgttttctatacaagTCTTCCTGTGACGACTATAATTTTTGACAAGGATATCTCTGAGGAAACAGTACTGCAATATCCCCAGATTTTACTCTATTCTCAGTCTGGAAG
                   |  |   |  ||| |||| |  |  ||||  |  |   |||   |     | |     ||    |   |  | | ||  | ||||       |  ||| ||||| || ||||| |||||  |||||||||||||| | ||||| ||  ||||  ||||||| ||||||||||||||||| ||| |||||||       |                                                                            
-------------------ttgttactgattatgaatgttctaatgctagataggcattccaatttctttatatagatctattctaaaaattttaaggtactgatg-gttgccttttcagTTTTTCATTTATTTCAGGTGTCTCTGGAACTAGCCTCTTCAATTCTGTTAGCTTGATGGCTTATAATGTTTTCTATACTAGTGTTCCTGTTCTAGTCAGT--------------------------------------------------------------------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactagcttgttcaactcaattagtctgatggcctataatgttttctatacaagTCTTCCTGTGACGACTATAATTTTTGACAAGGATATCTCTGAGGAAACAGTACTGCAATATCCCCAGATTTTACTCTATTCTCAGTCTGGAAG
                        gtctgat  putative branch site (score: 4)
                                        tgttttct  putative PPT
                                   tataatgttttctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtctcttgattctaatcctctttagttaggaatatcttttgctgtactgagcttctgctactgctttgcttttcccaccgccacctgtcaatgctgacctagcactcttttagtttctcctttatatcaggactctctggaactagcttgttcaactcaattagtctgatggcctataatgttttctatacaagTCTTCCTGTGACGACTATAATTTTTGACAAGGATATCTCTGAGGAAACAGTACTGCAATATCCCCAGATTTTACTCTATTCTCAGTCTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG