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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgccagagctccatatacgagcgacttatcgcgctgtgcctgtgcaagtgcttcgctttagatagattgctttgttttttgtgtactgatagatgtctcacaacacatgcag

Basic information

species Zea mays
transcript GRMZM2G082502_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082502_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os10g36780.2 (Oryza sativa), 5'ss of exon 11
CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgccagagctccatatacgag-----cgacttatcgcgctgtgcctgtgcaagtg---cttcgctttagatagat-tgctttgttttttg--tgtactgatagatgtctcacaacacatgcag
|||||||||| ||||| ||||||||||| ||||| ||||||||||||||||| || |||||||| |||||| | ||||||    | |      ||| ||| |       | ||| | ||  | | | |||  | |||   | | ||| |   |  || | || |  ||   |  || ||| |  || |     |||||  || ||
CTTCTAAAATAGTGTTCACAAATGGCTCTCAAGATCCATGGCGCCATGCCTCGAAACAGAAATCGTCGAAATATAgtgagctttcaaagttctcatctactaatatgttggcttgttgctatctccatgtttaggtgtagccttgctctttgtgtatctactctacttgcagcatgcactaactgaggctcgccaacatttgtag

upper sequence: GRMZM2G082502_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os10g36780.4 (Oryza sativa), 5'ss of exon 10
-------------------------CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgccagagctccatatacgagc-----gacttatcgcgctgtgcctgtgcaagt---gcttcgctttagatagat-tgctttgttttttg--tgtactgatagatgtctcacaacacatgcag
                         |||||||||| ||||| ||||||||||| ||||| ||||||||||||||||| || |||||||| |||||| | ||||||    | |      ||| ||| |       | ||| | ||  | | | |||  | ||   || | ||| |   |  || | || |  ||   |  || ||| |  || |     |||||  || ||
CGATTTTGCATGAAAAATGGTGCAGCTTCTAAAATAGTGTTCACAAATGGCTCTCAAGATCCATGGCGCCATGCCTCGAAACAGAAATCGTCGAAATATAgtgagctttcaaagttctcatctactaatatgttggcttgttgctatctccatgtttaggtgtagccttgctctttgtgtatctactctacttgcagcatgcactaactgaggctcgccaacatttgtag

upper sequence: GRMZM2G082502_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA16G24290.1 (Glycine max), 5'ss of exon 10
CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgccagagctccatatacgagcgacttatcgcgctgtgcctgtgcaagtgcttcgctttagatagattgctttgttttttgtgtactgatagatgtctcacaacacatgcag
 ||| |||||  | |||||||||||||| ||||| || ||||||||||| |||||||| |  |||||    || |||||||  ||||    |  |  |     | | |||         | |  ||  | |  |||  | |       |||   | | | | ||| |   |||  | ||| | | |  |    |
GTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATAgtgagtt-gcca----tttacttttcttcaattta---------gtcaatgacattcattcattatcc-----ttgtcatctctgtggtggatatatatttctctaaaatccaacatgg

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|71759256|gb|DR957193.1|DR957193
EST:     CTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA                         TGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGA
genomic: CTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgc ... acacatgcagTGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGA
EST: gi|91055261|gb|EB165679.1|EB165679
EST:     CTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA                         TGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATTTGA
genomic: CTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgc ... acacatgcagTGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGA
EST: gi|18180479|gb|BM381689.1|BM381689
EST:     CTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA                         TGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGA
genomic: CTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgc ... acacatgcagTGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGA
EST: gi|88750785|gb|DY534926.1|DY534926
EST:     CTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA                         TGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGA
genomic: CTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgc ... acacatgcagTGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGA
EST: gi|8367939|gb|BE050884.1|BE050884
EST:     CTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA                         TGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGA
genomic: CTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgc ... acacatgcagTGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGA

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 4 RNA-Seq libraries.


Block sizes: 37 (upstream exon), 43 (downstream exon)
Score: 30

CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgc ... acacatgcagTGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGAGGGGCTGTCCGCAGTGGCCTTTCAGGATCGAAG


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 36

CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgc ... acacatgcagTGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGAGGGGCTGTCCGCAGTGGCCTTTCAGGATCGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 42

CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgc ... acacatgcagTGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGAGGGGCTGTCCGCAGTGGCCTTTCAGGATCGAAG


Block sizes: 47 (upstream exon), 39 (downstream exon)
Score: 42

CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACAgtgagtccgc ... acacatgcagTGCCGTCGTACATAATGAAATGCAGAAACTGCGGACATGGGACTGATCTGAGGGGCTGTCCGCAGTGGCCTTTCAGGATCGAAG