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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatccttacatataaatctgtcggagttccaatttttaaccgatacaaatatttcctactatgttcattaaataccttgttgacaaaaccccgcagATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAACAACCTCAGTGCAAGCCACAAGTTTTCCGAAGCGTCTATGTTCATTGGC

Basic information

species Zea mays
transcript GRMZM2G033828_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033828_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 13
-----------------------------------gtatatccttacatataaat-ctgtcggagttccaatttttaaccgatacaaatatttcctactatgttcattaaataccttgttgacaaaaccccgcagATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAACAACCTCAGTGCAAGCCACAAGTTTTCCGAAGCGTCTATGTTCATTGGC
                                     || ||  |   ||| | | ||     |  |   | ||        | || |||| ||         ||| |   |   || |||    |     |||||| |||||| ||| |||  |||||||||| ||||||||||||||||| |||||| ||||||||||||||||||||||||| || || |||||||||||| 
gtctgtctagaaattactccccttgcaacaaagaaagatttcgcttgttatgattgctagtatatctatcaattgctgtttttccagatatctcagttagcactcagtt--ttgtttattggtccatgtgtgcagATATCTCAATTGGCACTGACATTCAAGGAAATTATTTTCGGCTACAGAAAACAATCTCAGTGCAAGCCACAAGTTTTCCGTAGTGTTTATGTTCATTGGG
















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|76933783|gb|DV173584.1|DV173584
EST:     ACAGGCACATTGACCAGATCATACTATGCAGCATATATGGAGTTGCCAAG                         ATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAA
genomic: ACAGGCACATTGACCAGATCATACTATGCAGCATATATGGAGTTGCCAAGgtatatcctt ... aaccccgcagATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAA
EST: gi|30087053|gb|CB885261.1|CB885261
EST:     ACAGGCACATTGACCAGATCATACTATGCAGCATATATGGAGTTGCCAAG                         ATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAA
genomic: ACAGGCACATTGACCAGATCATACTATGCAGCATATATGGAGTTGCCAAGgtatatcctt ... aaccccgcagATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAA
EST: gi|67026333|gb|CO455082.1|CO455082
EST:     ACAGGCACATTGACCAGATCATACTATGCAGCATATATGGAGTTGCCAAG                         ATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAA
genomic: ACAGGCACATTGACCAGATCATACTATGCAGCATATATGGAGTTGCCAAGgtatatcctt ... aaccccgcagATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAA
EST: gi|89756605|gb|DY686579.1|DY686579
EST:     ACAGGCACATTGACCAGATCATACTATGCAGCATATATGGAGTTGCCAAG                         ATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAA
genomic: ACAGGCACATTGACCAGATCATACTATGCAGCATATATGGAGTTGCCAAGgtatatcctt ... aaccccgcagATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAA

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: 45 (upstream exon), 48 (downstream exon)
Score: 99

GTATTCCCTTGTGCAGCAAATCCTTAGCCAACAGACTGGCCTTTTCTTCAACAGGCACATTGACCAGATCATACTATGCAGCATATATGGAGTTGCCAAGgtatatcctt ... aaccccgcagATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAACAACCTCAGTGCAAGCCACAAGTTTTCCGAAGCGTCTATGTTCATTGGC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 15

GTATTCCCTTGTGCAGCAAATCCTTAGCCAACAGACTGGCCTTTTCTTCAACAGGCACATTGACCAGATCATACTATGCAGCATATATGGAGTTGCCAAGgtatatcctt ... aaccccgcagATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAACAACCTCAGTGCAAGCCACAAGTTTTCCGAAGCGTCTATGTTCATTGGC


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 12

GTATTCCCTTGTGCAGCAAATCCTTAGCCAACAGACTGGCCTTTTCTTCAACAGGCACATTGACCAGATCATACTATGCAGCATATATGGAGTTGCCAAGgtatatcctt ... aaccccgcagATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAACAACCTCAGTGCAAGCCACAAGTTTTCCGAAGCGTCTATGTTCATTGGC


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 12

GTATTCCCTTGTGCAGCAAATCCTTAGCCAACAGACTGGCCTTTTCTTCAACAGGCACATTGACCAGATCATACTATGCAGCATATATGGAGTTGCCAAGgtatatcctt ... aaccccgcagATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAACAACCTCAGTGCAAGCCACAAGTTTTCCGAAGCGTCTATGTTCATTGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatacaaatatttcctactatgttcattaaataccttgttgacaaaaccccgcagATCTCTCAACTGGAACTTTCATTCAAGGAGATTATTTTCGGCTACAGGAAACAACCTCAGTGCAAGCCACAAGTTTTCCGAAGCGTCTATGTTCATTGGC
                                    tgttgac  putative branch site (score: 12)
                  tatgttcattaaata  TA-rich tract