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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacacatttgacacagttatacacctataccattagtgagcaatgcattattttcatgtaggataacataaatattcaaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGT

Basic information

species Zea mays
transcript GRMZM5G879882_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 4
gtataacacatttgacacagttatacacctat-accattagtgagcaatgcattattttcatgtaggataacataaatattcaacctt---cagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGT
|||  |  | || ||      ||||  ||||| | ||||   | ||| |||||||    ||| |||| | ||| ||||  ||||   |   |||||||| || ||||||||||| |  ||||| |||||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||||| || |||||||
gtaggatgccttgga------tatatgcctattatcatttaggggca-tgcattacccacatttaggctgacacaaattctcaaatcttatcagGTGTACTTCGAGTCAGAAGATGTCAAAGCATGCATTGTAACCTGCGGAGGCCTTTGCCCTGGGCTAAATACGGTCATTAGAGAGTTGGTGTGCGGCTTGT

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 4
gtataacacatttgacacagttatacacctataccattagtgagcaatgcattattttcatgtaggataacataaatattcaaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGT
       || | |    |  || |     |  |     | |||   ||| || ||    || ||  ||   |    || |      ||||||||||||||||||||| |||| | | || || |||||||| ||||| || || |||||||||||||| || |||||||| ||  | || |||||| | |
-----gtacgtcttcttcttttctcgcagtgcaagtggaatga-tgatgtatcatgcatatttactatgtaacttttaat-ggtgctcagGTGTATTTTGAGTCAGATGAAGTGCACGCATGTATTGTAACATGTGGTGGTCTGTGCCCTGGGCTCAACACAGTCATCAGGGAAATTGTGTGTGGCCTTT
















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|87153557|gb|DY398346.1|DY398346
EST:     AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGG                         GTGTATTTTGAGTCAGAAGAAGTGAAAGCTTGCATTGTAACCTGTGGAGGC
genomic: AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGGgtataacaca ... caaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGC
EST: gi|8367787|gb|BE050732.1|BE050732
EST:     AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGG                         GTGTATTTTGAGTCAGAAGAAGTGAAAGCTTGCATTGTAACCTGTGGAGGC
genomic: AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGGgtataacaca ... caaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGC
EST: gi|28873675|gb|CB329630.1|CB329630
EST:     AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGG                         GGGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGC
genomic: AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGGgtataacaca ... caaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGC
EST: gi|19436208|gb|BM952618.1|BM952618
EST:     AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGG                         GTGTATTTTGAGTCAGAAGAAGTGAAAGCTTGCATTGTAACCTGTGGAGGC
genomic: AGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGGgtataacaca ... caaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGC

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: 49 (upstream exon), 49 (downstream exon)
Score: 117

GTAGTTGTTCAGAAGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGGgtataacaca ... caaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

GTAGTTGTTCAGAAGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGGgtataacaca ... caaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

GTAGTTGTTCAGAAGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGGgtataacaca ... caaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 74

GTAGTTGTTCAGAAGAACAGTCCACGAGGAGTTCACTTCCGTCGTGCTGGACCTCGTCAGAGGgtataacaca ... caaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagtgagcaatgcattattttcatgtaggataacataaatattcaaccttcagGTGTATTTTGAGTCAGAAGAAGCGAAAGCTTGCATTGTAACCTGTGGAGGCCTTTGCCCTGGGCTCAATACTGTCATCAGAGAGTTGGTTTGTGGCTTGT
                             ggataac  putative branch site (score: 74)
                                                ccttc  putative PPT
                               ataacataaatattca  TA-rich tract