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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctagattctattgtgacactttgaatgtcattttctggatacctgaatataattttttaaggtctgacggtagccattctttcaatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT

Basic information

species Zea mays
transcript GRMZM5G840582_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 7
--------tgctagattctattgtgacactttgaatgtcattttctggatacc-tgaatataattttttaaggtctgacggtagccattctttcaatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT
        ||  ||||| || | ||| | |||| ||   |       |||||| |   | |  ||  ||  | ||| |       | |  ||||| | |||     ||||||||||| ||||||||||||||||||||||| | ||| ||||| |||||||| ||||| ||||||
tcatgtaatgtaagattttactttga-agtttggatagtagcac--agataccatttttctgtttgcttgtgatctaattacgttcctcatttca-tatga-----cagACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTT

upper sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 9
---tgctagattctattgtgacactttgaatgtcattttctggatacctgaatataattttttaaggtctgacggtagccattctttc-aatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT
     ||| ||   |      ||     | |||||  |  |  ||   || |     |    | |     |||| |   | ||  | |  ||||    ||||||||||| |||||||||||||||||||||||||||  ||| ||||| |||||||| |  ||||| |||
tgactctacatgtaaggtgttcatacaaattgtcacctcttcaatttttgcaacagctacactga----cgacgtttttcttttatcctgattttcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTT

upper sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA02G04320.2 (Glycine max), 3'ss of exon 9
---tgctagattctattgtgacactttgaatgtcattttctggatacctgaatataattttttaaggtctgacggtagccattctttc-aatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT
     ||| ||   |      ||     | |||||  |  |  ||   ||  ||||  ||         ||| | |   | ||  | |  ||||    ||||||||||| |||||||||||||||||||||||||||  ||| ||||| |||||||| |  ||||| |||
tgactctacatgtaaggtgttcatacaaattgtcacctcttcaatttttgc-tatagcttcactga---tgatgcttttcttttatcctgattttcttttgcagACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTT

upper sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv00s0225g00130.t01 (Vitis vinifera), 3'ss of exon 9
----tgctagattctattgtgacactttgaatgtcattttctggatacctgaatataattttttaaggtctgacggtagccattctttcaatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT
    || | ||   |    |   |     | ||  |||   |  || |    | | | | ||| ||    ||  | ||       |    |  |||  |||||||| || |||||||| || |||||||||||||||  ||| ||||| ||||| || ||||| || |||
ttattgttggaaaatgaaattcaagcacaattgaaattccttctattc----aaacagtgtttaaacaattggtgctaatttggatcatcaaatgatgttgcagACTGTTGATGAGATTTATAAGGTTGCATCAATATCACTCAGTCCAAATGTCCCTGGGCAGATATTT

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|78112475|gb|DV530869.1|DV530869
EST:     AGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAG                         ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
genomic: AGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAGgtatttgtta ... gagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
EST: gi|32850940|gb|CD990621.1|CD990621
EST:     AGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAG                         ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
genomic: AGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAGgtatttgtta ... gagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
EST: gi|91054117|gb|EB164535.1|EB164535
EST:     CAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAG                         ACAGTAGATGAGATATACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
genomic: CAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAGgtatttgtta ... gagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
EST: gi|7216933|gb|AW563070.1|AW563070
EST:     AGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAG                         ACAGTAGATGAGATATACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT
genomic: AGTGTGGACAACGTGGTGGATACTTCGAAATGACAAATCTTCCTCCAAAGgtatttgtta ... gagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatataattttttaaggtctgacggtagccattctttcaatttgagcttgcagACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT
                  gtctgac  putative branch site (score: 3)
     ataattttttaaggt  TA-rich tract