Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctcagctgttcttttgttggaggtctctcatgttactaccattgttattcttcataaaggaccatctatgtttagaaacttggcctgtttctct...

Basic information

species Oryza sativa
transcript LOC_Os01g56580.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G116086_T01 (Zea mays), 5'ss of exon 14
GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctcagctgttcttt-tgttggaggtctctcatgttactaccattgttattctt-cataaaggaccatctatgtttagaaacttggcctgtttctct
||||||||||||||||| ||||| ||||| |||||||||||||||||||| |||||||  ||||| ||||||||||||||||||||||||||| || |  |  || |   | | || |||| |||| || ||  |    || |||   |   || ||  |  ||  |    |    || | |     | ||| 
GATTGGATTATGGAGCAGTGGGAAAATAACTACTACATCAGTGCCATAGCTGGTGCAATGAATGGGAGTTCCTTGGTGGTCATGTCAAAAGgtctgccctaattgatggctgtatttgaggcctcttatatttat-tagttattacattcatatgaaaaaaaattgagtggtgtctacatagttaaatgctc-

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 14
GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctcagctgttcttttgttggaggtctctcatgttactaccattgttattcttcataaaggaccatctatgtttagaaacttggcctgtttctct
|| |||||||||||||| |||||||| |||||||| |||||| | ||||| || |||   ||||||||||||||||| |||||||| |||||| | |   | || |  |||| |         ||| |     ||| |||| |    ||  |   | |    || ||   |    | | ||   |||   |
GACTGGATTATGGAGCAGTGGGAGAAAAATTACTATATCAGTTCAATAGCTGGCGCAGTTAATGGAAGTTCCTTGGTTGTCATGTCCAAAGgtatataatatctataattttatgacctactcctccttcacatactattgattaatttatttttgaaatgcctttgcaaaatctccttgctattttactt

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 14
GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctcagctgttcttttgttgg-aggtctctcatgttactaccattgttattcttcataaaggaccatctat-gtttagaaacttggcctgtttctct
|||||||||||||| || ||||| || ||||||||||||||  | ||||| || ||  | ||||| ||||| ||||| |||||||| ||||||| |  |||  |   | |   |||  | | |  | ||  | ||    ||||   |||   |           | |  |||     ||     |   | |||
GATTGGATTATGGAACAGTGGGAAAAGAATTACTACATCAGCTCAATAGCAGGGGCTGCTAATGGGAGTTCTTTGGTTGTCATGTCTAAAGgtt-ggatcacattcccatagattgttaaggcatttattct-ctgtgtttgtctgtctgtttccttttttgcttctcattttttctctgcatttaactttct

upper sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 14
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 13
GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctcagctgttcttttgttggaggtctctcatgttactaccattgttattcttcataaaggaccatctatgtttagaaacttggcctgtttctct----
|| ||||| ||||| || ||||| || |||| ||| ||||||||||| || |||||||  || ||||| |||||||| |||||||| ||||||   | ||| | | | ||   ||  || |      | | | |  |||   |||       ||      || | | |   |   |||    | | |   |    
GAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAGgt--atttcacccgatgttacattt-agattaacactatcatt-tcatgcatatgtacttcaattttttatttttatcatgctgcttaatttttgtagatttat

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|58683649|gb|CK072336.1|CK072336
EST:     TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG                         GAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
genomic: TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctca ... ctctttccagGAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
EST: gi|218504544|gb|FG949399.1|FG949399
EST:     TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG                         GAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
genomic: TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctca ... ctctttccagGAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
EST: gi|218502457|gb|FG966789.1|FG966789
EST:     GCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGATGGTCATGTCAAAAG                         GAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
genomic: GCCATAGCGGGTGCAACAAATGGAAGTTCCTTGG-TGGTCATGTCAAAAGgtttgtctca ... ctctttccagGAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
EST: gi|58598509|gb|CK009037.1|CK009037
EST:     TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG                         GAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
genomic: TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctca ... ctctttccagGAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
EST: gi|218479830|gb|FG949479.1|FG949479
EST:     TGCCATAGCGGGTGCAACAAATGGAAG-TCCTTGGTGGTCATGTCAAAAG                         GAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
genomic: TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctca ... ctctttccagGAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
EST: gi|12623249|gb|AU173462.1|AU173462
EST:     TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG                         GAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
genomic: TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctca ... ctctttccagGAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
EST: gi|5005377|gb|AU070539.1|AU070539
EST:     TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG                         GAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
genomic: TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctca ... ctctttccagGAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
EST: gi|58609988|gb|CK038021.1|CK038021
EST:     TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAG                         GAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA
genomic: TGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctca ... ctctttccagGAACTCCTTACACTCAACAGTCTTACAAAGTTAGTGAATCGTTTCCCTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTGGATTATGGAGCAATGGGAGAATAATTACTACATCAGTGCCATAGCGGGTGCAACAAATGGAAGTTCCTTGGTGGTCATGTCAAAAGgtttgtctcagctgttcttttgttggaggtctctcatgttactaccattgttattcttcataaaggaccatctatgtttagaaacttggcctgtttctct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG