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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcggaacgcagtgcacagtaactgatttctttttatataataaatgcacgattgatatatacaagcttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGGAATCCAGACGGCCGAACATTCGCCACGGGGAACCAAGACAAGACGTGCA

Basic information

species Zea mays
transcript GRMZM2G113726_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113726_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g38880.3 (Oryza sativa), 3'ss of exon 7
gtaagcggaacgcagtgcacagtaactgatttct---------ttttatat---aataaatgcacgattgatatatacaagcttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGGAATCCAGACGGCCGAACATTCGCCACGGGGAACCAAGACAAGACGTGCA----
|||||| ||| |||  || |||  | | | |||            | | ||   |  ||| | |    | ||   |    | || ||||||||| |||||  ||||||  || ||| |||| ||||| || ||||| || ||||| ||||| ||||| |||||||| || || |||||||||||||| ||||    
gtaagcagaaagcaacgctcagcgattaacttccaaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgttt-ctcgcagacagTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGGAACCCAGATGGCCGGACATTCGCGACTGGTAACCAAGACAAGACATGCAGGAT

upper sequence: GRMZM2G113726_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g38880.6 (Oryza sativa), 3'ss of exon 7
gtaagcggaacgcagtgcacagtaactgatttct---------ttttatat---aataaatgcacgattgatatatacaagcttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGGAATCCAGACGGCCGAACATTCGCCACGGGGAACCAAGACAAGACGTGCA
|||||| ||| |||  || |||  | | | |||            | | ||   |  ||| | |    | ||   |    | || ||||||||| |||||  ||||||  || ||| |||| ||||| || ||||| || ||||| ||||| ||||| |||||||| || || |||||||||||||| ||||
gtaagcagaaagcaacgctcagcgattaacttccaaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgttt-ctcgcagACAGTTCATGAACTCCGCGGTCATCTGGACTACTCTTTCGCGTCAGCGTGGAACCCAGATGGCCGGACATTCGCGACTGGTAACCAAGACAAGACATGCA

upper sequence: GRMZM2G113726_T02 (Zea mays), 3'ss of exon 8
lower sequence: EFJ18234 (Selaginella moellendorffii), 3'ss of exon 8
gtaagcggaacgcagtgcacagtaactgatttcttttt----atataataaatgcacgattgatatatacaagcttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGGAATCCAGACGGCCGAACATTCGCCACGGGGAACCAAGACAAGACGTGCA
                | | | |   |  ||||  |      |  |   || |||         || |||   | |  |  |||  | |    |  ||| | |||||| | |||||||| ||||| ||||| ||| |||||||||||||||  ||||| || || ||||| |||| ||| ||| 
----------------gtatatttttttttttccatcccacgacttccaaagtgcttacacagcatttactttcgttgttccagGTGATAGCAACGCTCAAAGGCCATCTTGATTACTCTTTTGCTTCGGCCTGGCATCCAGACGGCCGAATCTTCGCGACTGGAAACCAGGACACGACTTGCC

upper sequence: GRMZM2G113726_T02 (Zea mays), 3'ss of exon 8
lower sequence: EFJ21971 (Selaginella moellendorffii), 3'ss of exon 8
gtaagcggaacgcagtgcacagtaactgatttctttttatataataaatgcacgattgatatatacaagcttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGGAATCCAGACGGCCGAACATTCGCCACGGGGAACCAAGACAAGACGTGCA
              ||  |   |   |    ||     |  |   || |||         || |||   | |  |  |||  | |    |  ||| | |||||| | |||||||| ||||| ||||| ||| |||||||||||||||  ||||| || || ||||| |||| ||| ||| 
--------------gtatattttttttcccatcccacgacttccaaagtgcttacacagcatttactttcgttgttccagGTGATAGCAACGCTCAAAGGCCATCTTGATTACTCTTTTGCTTCGGCCTGGCATCCAGACGGCCGAATCTTCGCGACTGGAAACCAGGACACGACTTGCC

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|18167290|gb|BM337129.1|BM337129
EST:     TGT-GGGGACCAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TGTGGGGGA-CAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|50330987|gb|CO526113.1|CO526113
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|56461997|gb|CK986295.1|CK986295
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|47961405|gb|CN844114.1|CN844114
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCANAA-CTCCATGGCCATTTGGATTACTCCNTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|44681734|gb|CK786782.1|CK786782
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|44682058|gb|CK787106.1|CK787106
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGNTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|47962732|gb|CN845441.1|CN845441
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
EST: gi|78024436|gb|DV492823.1|DV492823
EST:     TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAG                         ACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG
genomic: TTGTGGGGGACAGTCCTGATGGACTTCTGATTGACGCTAATTCAGGAAAGgtaagcggaa ... ttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatttctttttatataataaatgcacgattgatatatacaagcttgctcgcagACGGTTCACAAACTCCATGGCCATTTGGATTACTCCTTTGCGTCGGCATGGAATCCAGACGGCCGAACATTCGCCACGGGGAACCAAGACAAGACGTGCA
                            gattgat  putative branch site (score: 4)
                                            cttgctc  putative PPT
     ttctttttatataata  TA-rich tract