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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgccgccacgcacccccgtcatctctcctctcgacacggcacagctccacgtccgtctcgtttaactgaatgcctaaacacgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGGGCACCATGGTTGGGTACACCATCACGGCGACCATAAGCATGGC

Basic information

species Zea mays
transcript GRMZM5G830545_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G830545_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g65660.1 (Oryza sativa), 3'ss of exon 2
gtacgcgccgccacgcacccccgtcatctctcctctcgacacggcacagctccacgtccgtctcgtttaactgaatgcctaaacacgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGGGCACCATGGTTGGGTACACCATCACGGCGACCATAAGCATGGC
            | | || | |  ||| | |  ||||    |  ||      |  ||  ||     | |||  |||||| ||| |    |  ||||||| || ||||||||||||||||| |||||||||||||| |||||||||||||||||||| || ||||| ||||| || ||||||||||||| 
----------gtaagtacactca-cattttttttctctcatctccat-----cttgttggttaaactgaacgcaatgccaaaa-atatttt-cagGTCCTAGAGAGGTGTTCATGTGCGGAATCGCGCAGTACGTCAACCTGTGGGGCACCATGGTCGGCTACACAATCACCGCAACCATAAGCATGGT
















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|71448607|gb|DR829657.1|DR829657
EST:     CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcgccg ... cgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
EST: gi|89762390|gb|DY689996.1|DY689996
EST:     CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcgccg ... cgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
EST: gi|149007854|gb|EE040283.2|EE040283
EST:     CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcgccg ... cgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
EST: gi|148982434|gb|EE028315.2|EE028315
EST:     CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcgccg ... cgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
EST: gi|91051425|gb|EB161843.1|EB161843
EST:     CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcgccg ... cgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
EST: gi|148970844|gb|EE021618.2|EE021618
EST:     CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcgccg ... cgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
EST: gi|149078952|gb|EE167792.2|EE167792
EST:     CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCA                         GTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG
genomic: CACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcgccg ... cgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGG

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: 43 (upstream exon), 20 (downstream exon)
Score: 3

TACTACACCTCCACGCTGCTCGCCAACGCCTACCGCGCGCCGCACCCCGTCACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcgccg ... cgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGGGCACCATGGTTGGGTACACCATCACGGCGACCATAAGCATGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

TACTACACCTCCACGCTGCTCGCCAACGCCTACCGCGCGCCGCACCCCGTCACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcgccg ... cgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGGGCACCATGGTTGGGTACACCATCACGGCGACCATAAGCATGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 34

TACTACACCTCCACGCTGCTCGCCAACGCCTACCGCGCGCCGCACCCCGTCACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcgccg ... cgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGGGCACCATGGTTGGGTACACCATCACGGCGACCATAAGCATGGC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 35

TACTACACCTCCACGCTGCTCGCCAACGCCTACCGCGCGCCGCACCCCGTCACCGGCGACAGGAACCGCACCTACATGGACGCCGTCAGATCGTACCTCAgtacgcgccg ... cgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGGGCACCATGGTTGGGTACACCATCACGGCGACCATAAGCATGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggcacagctccacgtccgtctcgtttaactgaatgcctaaacacgcatcgcagGTCCCAGGGAGGTGTTCATGTGCGGGATCGCGCAGTACGTGAACCTGTGGGGCACCATGGTTGGGTACACCATCACGGCGACCATAAGCATGGC
                                    gcctaaa  putative branch site (score: 35)
                         tttaact  TA-rich tract