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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTACCCATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAACATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgtaagttggtctgtttcagcatagaataaaataatttagcaagcacttgtctaacagtttttttttttcaaatcag

Basic information

species Zea mays
transcript GRMZM2G000645_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 10
AGTACCCATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAACATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgtaagttggtctgtttcagcatagaataaaataatttagcaagca--cttgtctaacagtttttt---tttttcaaatcag
||||||  | ||||| ||||||||| |||| |||||||||||||| |||||||| || ||||| ||||| || ||||| || || |||||||| ||||| || |||||| ||||||    | |||||  |  |||  | ||   |  ||  ||| |     |  |   ||||   | ||||
AGTACCTGTGGCAAGCATGGATACCAGTGGAAAAATCATTTGGGCAAAACATAACGAGATACAGACTGTGAACATCAAAACTGTTGGTGCAGGCTTTGAGgtcagttggcctgtttgcaaacagaatcgatcaatcaaacagagaagctgatctcatgccctactatgttttcttattcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 10
AGTACCCATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAACATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgtaagttggtctgtttcagcatagaataaaataatttagcaagcacttgtctaacagtttttttttttcaaat-cag----------------
|| |||  |||| || ||||||| | |||||||||| |||||||| || ||||||||||| |||||||| ||||| | ||  || || |||| | | || ||| |      | |||   | |    |      | |  | |||||   ||  ||   |  |||  |  || || ||                 
AGAACCTGTAGCCAGCATGGATAACAGTGGGAAAATAATTTGGGCTAAGCATAATGAAATTCAAACTGTCAATATAAGGAGTGTAGGAGCAGATGTGGAGgtatgggctcatttttaccctttttgtccgtgtaatatgtaagcaaaagtggaaacttgctttagtgacacatgcaagtattatgttttttag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 10
AGTACCCATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAACATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgta--agttggtctgtttcagcatagaataaaataatttagcaagcacttgtctaacagtttttttttttcaaat-cag----------------
|| |||  |||| || ||||||| | |||||||||| |||||||| || ||||||||||| |||||||| ||||| |  |  || || |||| | | || |||   | |  | | |  |    |  |      |||| | | |||||   ||  ||   |  |||  |  || || ||                 
AGAACCTGTAGCCAGCATGGATAACAGTGGGAAAATAATTTGGGCTAAGCATAATGAAATTCAAACTGTCAATATAAGAAGTGTAGGAGCAGATGTGGAGgtatgggctcatttttacctttttttatccgtctaatat-gtaagcaaaagtggaaacttgctttagtgacacatgcaagtactatgttttttag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S79_180V6.2 (Physcomitrella patens), 5'ss of exon 10
AGTACCCATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAACATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgtaag---ttggtctgtttcagcat-agaataaaataatttagcaagcacttgtctaacagtttttttttttcaaatcag----------------------------------------------------------------------------------------
 | |||  | || || ||||||    |||| |||||||| ||||| ||||| ||||||||||| ||||| ||| ||||| |||| ||||| | ||| || ||      |    |||||| |  || ||| | ||||||  |     | | |||| | | | ||| |||  |    |                                                                                            
GGCACCAGTTGCTAGCATGGATGGTAGTGGTAAAATCATATGGGCAAAACACAATGAAATACAGACTGTCAATGTCAAGGCAGTTGGTGCTGATTTCGAGgtggcgcctactcctgtttaaaaattagattcaaataaagttagttgtatttgttttatactttctttcctgtgcaatgttagttatcattagctatatttagaactatcatgtagtaatatcaaataactgaagctttttcatgtttttatttttatttttgtgcag

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|26457397|gb|CA828980.1|CA828980
EST:     ATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAA                         GCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGT
genomic: ATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgtaagttggt ... ttcaaatcagGCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGT
EST: gi|32865242|gb|CF004924.1|CF004924
EST:     ATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAA                         GCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGT
genomic: ATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgtaagttggt ... ttcaaatcagGCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGT
EST: gi|31353243|gb|CD437600.1|CD437600
EST:     ATAATGAAATACAAACTGTAAATATCAACTCTGTCGGTGCAGGCTTTGAA                         GCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGT
genomic: ATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgtaagttggt ... ttcaaatcagGCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGT

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: 47 (upstream exon), 49 (downstream exon)
Score: 247

AGTACCCATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAACATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgtaagttggt ... ttcaaatcagGCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

AGTACCCATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAACATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgtaagttggt ... ttcaaatcagGCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

AGTACCCATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAACATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgtaagttggt ... ttcaaatcagGCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

AGTACCCATAGCAAGTATGGATACCGGTGGGAAAATCATTTGGGCGAAACATAATGAAATACAAACTGTAAATATCAAGACAGTCGGTGCAGGTTTTGAAgtaagttggt ... ttcaaatcagGCCACAGATGGAGAAAGATTACCCTTGGCTGTAAAAGAGTTAGGAAGCTGTGATTTGTACCCACAG