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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTGGGAAACAAGCGCACTACTGCTATGATGATGCTGACCTTAAGGAGCTAGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAGgtacaaacatttgaatcaatcaactaatgagtgcaatgaactttgagaaaatctgtcaacacatcacagtcatttctcagtacatttggctatttgttat...

Basic information

species Oryza sativa
transcript LOC_Os01g16290.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16290.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G111014_T01 (Zea mays), 5'ss of exon 19
CGTGGGAAACAAGCGCACTACTGCTATGATGATGCTGACCTTAAGGAGCTAGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAGgtacaaacatttgaatcaatcaactaatgag--tgcaatgaactttgagaaaatctgtcaacacatcacagtcatttctcagtacattt--ggctatttgttat--
||||| |||| ||| || ||||||||||||||||| ||||| || ||| ||||||||||||||||  ||||||| || ||||||||||| |||||||||||||||     || ||  | | ||| ||||||  |  ||  || | |      |  |   || ||||     | | |||   | ||||||     |   |  |||  
CGTGGAAAACTAGCACATTACTGCTATGATGATGCCGACCTCAAAGAGATAGTTAACACCTTCCCTGCAAATGCATCATATCATATCCAGAGGTTTAAAGgtaca-----tttaactattgaac-aatgagcttctaagaaaatatcctggcacataaaaaaacatttttcttacttcagtgcacatttttaattgccttctattt

upper sequence: LOC_Os01g16290.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA19G31030.1 (Glycine max), 5'ss of exon 19
CGTGGGAAACAAGCGCACTACTGCTATGATGATGCTGACCTTAAGGAGCTAGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAGgtacaaacatttgaatcaatcaactaatgagtgcaatgaactttgagaaaatctgtcaacacatcacagtcatttctcagtacatttggctatttgttat--
 | || ||||||| |||||| |||||||||||||||||||||||  ||||    |   | |||||  | ||||| || ||  | || |||||||| |||||||  |  |    | | | |  | |     |    |  ||  ||   |   |     ||||      |   | |      || ||    | || | ||||  
AGGGGAAAACAAGTGCACTATTGCTATGATGATGCTGACCTTAAAAAGCTTCAAAGATCATTCCCTCCTAATGCATCATACAACATGCAAAGGTTCAAAGgtatgatgag--aagttattttagttgcatgcattagaaatatttgtaggcttgtataacaatcttgacaaaataaattttatataaaacaatatcttattt

upper sequence: LOC_Os01g16290.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA03G28290.1 (Glycine max), 5'ss of exon 19
CGTGGGAAACAAGCGCACTACTGCTATGATGATGCTGACCTTAAGGAGCTAGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAGgtacaaacatttgaatcaatcaactaatgagtgcaatgaactttgagaaaatctgtcaac--acatcacagtcatttctcagtacattt--ggctatttgttat
 | || ||||||| |||||| |||||||||||||||||||||||  ||||    |   | |||||  | ||||| || ||  | || |||||||| |||||||  |  |    | | | |  | |  |   ||||     | ||   || || |||   |    || ||| || |  |  | || ||||      |     |||
AGGGGAAAACAAGTGCACTATTGCTATGATGATGCTGACCTTAAAAAGCTTCAAAGATCATTCCCTGCTAATGCATCATACAACATGCAAAGGTTCAAAGgtatgatgaa--aagttattttagt--ttcatgcatcttgccttagaaatatttgttggcttgtataacaatcttgacaaaataaattttaaataaagcaatat

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|33800991|gb|CF326369.1|CF326369
EST:     AGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAG                         GTCTTGGTGAGATGATGCCGGCACAATTATGGGAGACAACAATGGACCCTG
genomic: AGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAGgtacaaacat ... ggctaaatagGTCTTGGTGAGATGATGCCGGCACAATTATGGGAGACAACAATGGACCCTG
EST: gi|88846177|gb|CI372945.1|CI372945
EST:     AGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAG                         GTCTTGGTGAGATGATGCCGGCACAATTATGGGAGACAACAATGGACCCTG
genomic: AGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAGgtacaaacat ... ggctaaatagGTCTTGGTGAGATGATGCCGGCACAATTATGGGAGACAACAATGGACCCTG
EST: gi|66923153|gb|CX110001.1|CX110001
EST:     AGTTAACACCTTCCCAACAAATGCTTCTTATCATATTCAAAGGTTTAAAG                         GTCTTGGTGAGATGATG
genomic: AGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAGgtacaaacat ... ggctaaatagGTCTTGGTGAGATGATG
EST: gi|218495419|gb|FG960500.1|FG960500
EST:     AGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAG                         GTCTTGGTGAGATGATGCCGGCACAATTATGGGAGACAACTATGGACCCTG
genomic: AGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAGgtacaaacat ... ggctaaatagGTCTTGGTGAGATGATGCCGGCACAATTATGGGAGACAACAATGGACCCTG
EST: gi|89185707|gb|CI047576.1|CI047576
EST:     AGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAG                         GTCTTGGTGAGATGATGCCGGCACAATTATGGGAGACAACAATGGACCCTG
genomic: AGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAGgtacaaacat ... ggctaaatagGTCTTGGTGAGATGATGCCGGCACAATTATGGGAGACAACAATGGACCCTG
EST: gi|86882357|gb|CI325783.1|CI325783
EST:     AGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAG                         GTCTTGGTGAGATGATGCCGGCACAATTATGGGAGACAACAATGGACCCTG
genomic: AGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAGgtacaaacat ... ggctaaatagGTCTTGGTGAGATGATGCCGGCACAATTATGGGAGACAACAATGGACCCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 62 (upstream exon), 73 (downstream exon)
Score: 27

CGTGGGAAACAAGCGCACTACTGCTATGATGATGCTGACCTTAAGGAGCTAGTTAACACCTTCCCAACAAATGCTTCTTATCATATCCAAAGGTTTAAAGgtacaaacat ... ggctaaatagGTCTTGGTGAGATGATGCCGGCACAATTATGGGAGACAACAATGGACCCTGAGAGGAGGATGTTGAAGCAGCTAAAGGTTGAAGATGCTGCTGAGGCCAA




<











<


<