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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctcataagtcgctcctcctgaaatttctgtgcattttgtgcgctgcttctaactgaaacctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA

Basic information

species Zea mays
transcript GRMZM2G062210_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062210_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g02540.1 (Oryza sativa), 3'ss of exon 5
----gtaaatctcataagtcgctcctcctgaaatttctgtgcattttgtgcgctgcttctaactgaaacctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA
     | |  |||    | || | | |  |  ||| | |    | ||  |   ||||  ||  |||    ||||||||| ||||||||||||||||||||||| ||||| || |||||||||||||| |||||||||||||| || |||||||||||||| |||||||| |||||||
gtactttatcctctattggcgatgc-ctagggattccaggttgtgttaggttttgctcatatgtgat-tttctgcagGCTCGGATAGACTCCCACAACAAGATTCTTTATGCGAGGCATGCTGACCAAAGAAATGCAACTTTTCAACGTGTCCTTCAAACAGGCAATGAGTTTGAGA

upper sequence: GRMZM2G062210_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ06457 (Selaginella moellendorffii), 3'ss of exon 5
gtaaatctcataagtcgctcctcctgaaatttctgtgcattttgtgcgctgcttctaactgaaacctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA
||||     |  | | |   ||  |  | |||||    | | |   || || | |               ||||||||||| ||||||||||||||||| || |||||  | || ||||||||  | || ||| | || || || | | | ||||| ||| | |||||  || 
gtaagctagaacaatggtggctgtt--agtttct---tactcttcacgttgttgc---------------cagGCCCGGATCGACTCCCACAACAAGATTCTCTACGCTCGCCACGCTGACCAACGCAAGGCATCGTTTCAACGCGCCATGCAAACAGGCTACGACTTCCAGC

upper sequence: GRMZM2G062210_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ08729 (Selaginella moellendorffii), 3'ss of exon 5
gtaaatctcataagtcgctcctcctgaaatttctgtgcattttgtgcgctgcttctaactgaaacctctgc-agGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA
                        | |  |   ||     ||| |  | | |||     | |      ||| |||||||||| ||||||||||||||||| || |||||  | || ||||||||  | || ||| | || || || | | | ||||| ||| | |||||  || 
-----------------------gtaagctagatggatggttttttagtttcttactcttcacgttgttgccagGCCCGGATCGACTCCCACAACAAGATTCTCTACGCTCGCCACGCTGACCAACGCAAGGCATCGTTTCAACGCGCCATGCAAACAGGCTACGACTTCCAGC

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|32866164|gb|CF005846.1|CF005846
EST:     CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAG                         GCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG
genomic: CCATGCTGCAGAAGGAGCTGGCCGCACTGATTACTGAGGACAAAATACAGgtaaatctca ... acctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctcctgaaatttctgtgcattttgtgcgctgcttctaactgaaacctctgcagGCCCGGATAGACTCCCACAACAAGATCCTTTACGCAAGGCATGCTGACCAGAGAAATGCAACTTTCCAGCGTGTCCTTCAAACCGGCAATGACTTTGAGA
                                  ttctaac  putative branch site (score: 1)
                                              cctctgc  putative PPT
      tgaaattt  TA-rich tract