Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggcactagtttttagtatgatcattatgacatgtttttcacctgggtgtttctgatttccttttcatctgtatagGTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAGTTCAGTAATTGGACCCTCATTGGATCACTGACTGCGTCTGGACTGCCTG

Basic information

species Zea mays
transcript GRMZM2G403915_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G403915_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g36390.1 (Oryza sativa), 3'ss of exon 2
gtctggcactagtttttagtatgatcattatgacatgtttttcacctgggtgtttctgatttccttttcatctgtatagGTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAGTTCAGTAATTGGACCCTCATTGGATCACTGACTGCGTCTGGACTGCCTG
||||||    |  ||||| | || ||    | |  |||| || |||||| ||||||||||    | |   | || ||||||||| |||||| ||||||||||| | ||||| ||||||||||| || || |||| ||||||||   |||   ||||||| ||||| || ||||| || |
gtctggtcagaagttttatt-tggtc----taaattgttcttgacctggctgtttctgatagaatgtgtgtttgcatagGTTATATGTGCAGTCATTTTATTGGTGGCAGAAGGTAGTCTGAAGAAGCAATTCAATAATTGGAGTATCACCAGATCACTTACTGCATCAGGACTTCCCG
















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|211421462|gb|FL302147.1|FL302147
EST:     CCAAGATACTATAGTGACTTCACTCGTTCTTGCAACGGAAGCAGCAAAG                         GTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAG
genomic: CCAAGATACTATAGTGACTTCACTCGTTCTTGCAACGGAAGCAGCAAAGgtctggcact ... atctgtatagGTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAG
EST: gi|211424049|gb|FL302150.1|FL302150
EST:     CCAAGATACTATAGTGACTTCACTCGTTCTTGCAACGGAAGCAGCAAAG                         GTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAG
genomic: CCAAGATACTATAGTGACTTCACTCGTTCTTGCAACGGAAGCAGCAAAGgtctggcact ... atctgtatagGTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAG
EST: gi|211424048|gb|FL302149.1|FL302149
EST:     CCAAGATACTATAGTGACTTCACTCGTTCTTGCAACGGAAGCAGCAAAG                         GTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAG
genomic: CCAAGATACTATAGTGACTTCACTCGTTCTTGCAACGGAAGCAGCAAAGgtctggcact ... atctgtatagGTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAG
EST: gi|211421463|gb|FL302148.1|FL302148
EST:     CCAAGATACTATAGTGACTTCACTCGTTCTTGCAACGGAAGCAGCAAAG                         GTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAG
genomic: CCAAGATACTATAGTGACTTCACTCGTTCTTGCAACGGAAGCAGCAAAGgtctggcact ... atctgtatagGTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAG

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), 43 (downstream exon)
Score: 75

CCAAGATACTATAGTGACTTCACTCGTTCTTGCAACGGAAGCAGCAAAGgtctggcact ... atctgtatagGTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAGTTCAGTAATTGGACCCTCATTGGATCACTGACTGCGTCTGGACTGCCTG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 44

CCAAGATACTATAGTGACTTCACTCGTTCTTGCAACGGAAGCAGCAAAGgtctggcact ... atctgtatagGTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAGTTCAGTAATTGGACCCTCATTGGATCACTGACTGCGTCTGGACTGCCTG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 60

CCAAGATACTATAGTGACTTCACTCGTTCTTGCAACGGAAGCAGCAAAGgtctggcact ... atctgtatagGTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAGTTCAGTAATTGGACCCTCATTGGATCACTGACTGCGTCTGGACTGCCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 43

CCAAGATACTATAGTGACTTCACTCGTTCTTGCAACGGAAGCAGCAAAGgtctggcact ... atctgtatagGTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAGTTCAGTAATTGGACCCTCATTGGATCACTGACTGCGTCTGGACTGCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattatgacatgtttttcacctgggtgtttctgatttccttttcatctgtatagGTTATTTGTGCAATCATTTTATTGATTGCAGACGGTAGTCTGAAAAAACAGTTCAGTAATTGGACCCTCATTGGATCACTGACTGCGTCTGGACTGCCTG
                             ttctgat  putative branch site (score: 43)
                            tttctgatttcctttt  CT-rich tract
          atgttttt  TA-rich tract