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

ACCCTAGGAATAGACCATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcaccccctccttttttttcttccttgggtcatagtcaggattagagctatgctgatgtgctgccttcccag

Basic information

species Zea mays
transcript GRMZM2G145107_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145107_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g58080.1 (Oryza sativa), 5'ss of exon 2
ACCCTAGGAATAGACCATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtc--------------accccctccttttttttcttccttgg---gtcatagtcaggattagagctatgctgatgtgctgccttcccag------------
|||||||||||||||||||||||||||||||| |||||||| ||||| ||||| ||||||||||||||||||               |  ||    |||||||| || | |     | |||   ||  | |  |   |   |  | |  |    ||||              
ACCCTAGGAATAGACCATGCCATGGCATCATTCATTTGGCTTTGTGGACCTATTACTGGTTTTGTGgtaagtttctgcaataattaaattcctcttttttttttgtttcataaccaggcatgtccaacactccaaacacaatagtatattaatgtcccgtgattctctgcag
















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|78120050|gb|DV538434.1|DV538434
EST:     ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTG                         GTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
genomic: ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
EST: gi|93282781|gb|EB675045.1|EB675045
EST:     ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTG                         GTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
genomic: ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
EST: gi|93284115|gb|EB676379.1|EB676379
EST:     ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTG                         GTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
genomic: ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
EST: gi|19855127|gb|BQ060179.1|BQ060179
EST:     ATGCCATGGCACCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTG                         GTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCGAAGTATGGG
genomic: ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
EST: gi|78078077|gb|DV506492.1|DV506492
EST:     ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTG                         GTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
genomic: ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
EST: gi|149104737|gb|EE290188.2|EE290188
EST:     ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGGTTTGGG                         GTTCAACCTTGTGTTGGTGT
genomic: ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGT

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: 44 (upstream exon), 49 (downstream exon)
Score: 44

ACCCTAGGAATAGACCATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGGAGGAGAAGACCATTTATTTTGGCTGGATGCATAATGATATGTGCTGCT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 55

ACCCTAGGAATAGACCATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGGAGGAGAAGACCATTTATTTTGGCTGGATGCATAATGATATGTGCTGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 57

ACCCTAGGAATAGACCATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGGAGGAGAAGACCATTTATTTTGGCTGGATGCATAATGATATGTGCTGCT


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 110

ACCCTAGGAATAGACCATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGGAGGAGAAGACCATTTATTTTGGCTGGATGCATAATGATATGTGCTGCT