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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCTCACCCAAATCGAGAGGTATTTGAAGCAAGCCATTGTTGACAAGAATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctgcagttatattttgtgctccagttggatatattgttactagttggtgcagctatagatatttttattatgttttccacatgtttgtattattggcag

Basic information

species Zea mays
transcript GRMZM2G178618_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 5'ss of exon 5
CCTTCTCACCCAAATCGAGAGGTATTTGAAGCAAGCCATTGTTGACAAGAATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctgcagttatattttgtgctccagttggatatattgttactagttggtgcagctatagatatttttattatgttttccacatgtttgtattattggcag
 ||||| |||||||| || || ||||||||||||||||||||||||||||| ||||||||||| || |||||||||||||||||||||||||||||||| |||||| |   |  | || | | |||     |   ||    | ||||     |   ||  |    | |     | | | || |    ||| || |||| |  ||||
ACTTCTAACCCAAATTGAAAGATATTTGAAGCAAGCCATTGTTGACAAGAACCCTGTTGTTGCAAGCGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAGgtatgtgcaaaacgtttagtctttgcctttatgcaattgcatattacagccagacccaaatccttaca-----aatgttttgtttgtatggttttattctgagcag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G01470.1 (Glycine max), 5'ss of exon 5
CCTTCTCACCCAAATCGAGAGGTATTTGAAGCAAGCCATTGTTGACAAGAATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtat--gtcctgc-agttatattttgtgctccagttggatatattgttactagttggtgcagctatagatatttttattatgttttccacatgtttgtattattggcag
||| ||  | ||||| ||||||||||| || ||||||||||| || || ||||| |||||||| ||||| || || |||||||||||  |  | || || |||   ||| | | | ||   ||||||  ||    || ||||||  | | || |   | |    || | |  ||  |                                
CCTCCTTTCACAAATTGAGAGGTATTTAAAACAAGCCATTGTAGATAAAAATCCAGTTGTTGCAAGTGCTGCTCTAGTTAGTGGCATTCATCTACTCCAGgtaatagtcatactaatttccttttgtaatc----tgtatatatcctca-tattcattacgctgattgcttattacag-------------------------------

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 5
CCTTCTCACCCAAATCGAGAGGTATTTGAAGCAAGCCATTGTTGACAAGAATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctgcagttatattttgtgctccagttggatatattgttactagttggtgcagctatagatatttttattatgttttccacatgtttgtattattggcag
 || || || ||||| ||| | ||| |||| || || ||||| ||||||||||| |||||||| ||||| ||||| ||||| |||||  |  | || || ||||   |   |  ||| | |  | |   |  |    |||||        |  |||  ||      |  || | ||||||   || | | |  |            
TCTCCTTACTCAAATAGAGCGATATCTGAAACAGGCTATTGTAGACAAGAATCCAGTTGTTGCAAGTGCAGCCCTAGTTAGCGGCATTCATATACTCCAGgtattaacaaaatctatttgtaattccttatct---catatt-----ccatatgtgttgcc-----tgcttattttatgtccccc-cttatcag------------

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G01520.1 (Glycine max), 5'ss of exon 5
CCTTCTCACCCAAATCGAGAGGTATTTGAAGCAAGCCATTGTTGACAAGAATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtat--gtcctgc-agttatattttgtgctccagttggatatattgttactagttggtgcagctatagatatttttattatgttttccacatgtttgtattattggcag
||| ||  | ||||| ||||||||||| || ||||||||||| || || ||||| |||||||| ||||| || || |||||||||||  |  | || || |||   ||| | | | ||   ||||||  | |  ||  ||||  |  || |  |   |||  || |   ||||                                    
CCTCCTTTCACAAATTGAGAGGTATTTAAAACAAGCCATTGTAGATAAAAATCCAGTTGTTGCAAGTGCTGCTCTAGTTAGTGGCATTCATCTACTCCAGgtaatagtcatactaatttccttttgtaattct-ttatatatcctcatattcatctatgcttct-tgcttattacag--------------------------------

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA11G12610.2 (Glycine max), 5'ss of exon 5
CCTTCTCACCCAAATCGAGAGGTATTTGAAGCAAGCCATTGTTGACAAGAATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctgcagttatattttgtgctccagttggatatattgttactagttggtgcagctatagatatttttattatgttttccacatgtttgtattattggcag
 || || || ||||| ||| | ||| |||| ||||| ||||| ||||||||||| || ||||| ||||| ||||| ||||| |||||  |  | || || ||||       | | | || |  || |  | ||   ||| |  |         |||  ||      |  || |  |||||   || | | |  |            
TCTCCTTACTCAAATTGAGCGATATCTGAAACAAGCTATTGTAGACAAGAATCCAGTCGTTGCAAGTGCAGCCCTGGTTAGCGGCATTCATATACTCCAGgtat------tattaaaatctattggt--aattccttatctcatattccacatgtgttgcc-----tgcttattctatgtccccc-cttatcag------------

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 5'ss of exon 5
CCTTCTCACCCAAATCGAGAGGTATTTGAAGCAAGCCATTGTTGACAAGAATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctgcagttatattttgtgctccagttggatatattgttactagttggtgcagctatagatatttttattatgttttccacatgtttgtattattggcag
|||||||||||| || ||| | || ||||| ||||| || ||||||||||| ||||||||||| ||||| || ||||| ||||| ||  |  | || || |||      |    | | |    |  |    ||  || |||  |   ||  |  | |   || |     |  || |||| ||   |  | |||| ||         
CCTTCTCACCCAGATTGAGCGATACTTGAAACAAGCAATAGTTGACAAGAACCCTGTTGTTGCAAGTGCAGCTCTTGTCAGTGGAATTCATCTTCTCCAGgtacaattgggttgtgtgtagattttttttattctatttat-atatttaaattatcctcttacatgctctaataatatgattattatttttttggatag-------

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S15_298V6.2 (Physcomitrella patens), 5'ss of exon 4
CCTTCTCACCCAAATCGAGAGGTATTTGAAGCAAGCCATTGTTGACAAGAATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgta-tgtcctgcagttatattttgtgctccagttggatatattgttactagttggtgcagctatagatatttttattatgttttccacatgtttgtattattggcag
 ||  |   |||||| ||| ||||| ||||||||||  | || |||||||||||||||||| |||| ||||| ||||| || || ||| |  | || || ||| | | ||| ||    ||| | |  | |  |     |  ||     |  || |  | |   |  |   || ||||    ||   | || |||||    |      
GCTGTTGGGCCAAATTGAGCGGTATCTGAAGCAAGCTGTCGTGGACAAGAATCCTGTTGTTTCCAGCGCGGCACTTGTCAGCGGTATCCATCTTCTACAGgtactattctgaagagggattat-tattactttcaagaactttcaagatccttaggcctgtattgcaagattatatttgtattctgatatttttgttccct------

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|18655281|gb|BM500086.1|BM500086
EST:     ATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAA                         ACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTG
genomic: ATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctg ... ttattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTG
EST: gi|148956209|gb|EC901999.2|EC901999
EST:     ATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAA                         ACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTG
genomic: ATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctg ... ttattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTG
EST: gi|22490147|gb|BU050070.1|BU050070
EST:     ATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAA                         ACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTG
genomic: ATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctg ... ttattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTG
EST: gi|148931355|gb|EC874250.2|EC874250
EST:     ATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAA                         ACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTG
genomic: ATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctg ... ttattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTG
EST: gi|87153597|gb|DY398386.1|DY398386
EST:     ATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAA                         ACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTG
genomic: ATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctg ... ttattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTG
EST: gi|60396049|gb|DN228919.1|DN228919
EST:     TGGCATCTACTTGCTTC-A                         ACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTG
genomic: TGGCATCTACTTGCTTCAAgtatgtcctg ... ttattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTG

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: 48 (upstream exon), 49 (downstream exon)
Score: 282

CCTTCTCACCCAAATCGAGAGGTATTTGAAGCAAGCCATTGTTGACAAGAATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctg ... ttattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 303

CCTTCTCACCCAAATCGAGAGGTATTTGAAGCAAGCCATTGTTGACAAGAATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctg ... ttattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 167

CCTTCTCACCCAAATCGAGAGGTATTTGAAGCAAGCCATTGTTGACAAGAATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctg ... ttattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 373

CCTTCTCACCCAAATCGAGAGGTATTTGAAGCAAGCCATTGTTGACAAGAATCCTGTTGTTGCCAGTGCGGCCCTTGTTAGTGGCATCTACTTGCTTCAAgtatgtcctg ... ttattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACC