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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actagaattgggtcccatatgtatgaggtgaaagatgttcctttttagatcggtactgatttgattgtaacctttgccttttgtttctttacctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCCAAAACTGGGACTGGTAAAACTTTGGCATTTGGAATCCCCATAATGGATG

Basic information

species Zea mays
transcript GRMZM2G107984_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107984_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g41715.1 (Oryza sativa), 3'ss of exon 1
actagaattgggtcccatatgtatga-ggtgaaagatgttcctttttagatcggtactgatttgattgtaacctttgccttttgtttctttac-ctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCCAAAACTGGGACTGGTAAAACTTTGGCATTTGGAATCCCCATAATGGATG
     ||| |  |   | ||  | |    |   | || ||   |    | |   |  || ||   |  ||| | | | ||| |||||   | | || | ||||||||||||||||| |||||||||||||||| |||||||||||| ||||||||||| || || || || |||||||| ||||||||||||||| |||| |
-tggcaatagcataggacattcaagttactttcatatattaagtcaacggttcattttg-ttcagtaataatcatggacttatgttttgctgctctgcgcagAGAGCTGTCCTTGAACCAGCAATGCAAGGAAAGGACATGGTTGGTCGTGCCAAAACAGGTACAGGAAAGACTTTGGCTTTTGGAATCCCCATACTGGACG
















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|149061229|gb|EE157494.2|EE157494
EST:     TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAG                         AGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
genomic: TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
EST: gi|211281261|gb|FL322092.1|FL322092
EST:     TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAG                         AGAGCTGTCCTTGAGCCGGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
genomic: TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
EST: gi|149089755|gb|EE179029.2|EE179029
EST:     TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAG                         AGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
genomic: TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
EST: gi|211017399|gb|FL066295.1|FL066295
EST:     TCGTCGAAAGGCTCGCCAGCAAGGGCATCAACAAGCTGTTCCCCATCCAG                         AGAGCTGTCCTTGAGCCGGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
genomic: TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
EST: gi|14191124|gb|BG833354.1|BG833354
EST:     GCTGTTCCCCATCCAG                         AGAGCTGTCCTTGAGCCAGCAATGCAAGGCAAGGGACATGGTTGGCCGTGC
genomic: GCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGG-AAGGGACATGGTTGGCCGTGC
EST: gi|211017398|gb|FL066294.1|FL066294
EST:     TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAG                         AGAGCTGTCCTTGAGCCGGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
genomic: TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagatcggtactgatttgattgtaacctttgccttttgtttctttacctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCCAAAACTGGGACTGGTAAAACTTTGGCATTTGGAATCCCCATAATGGATG
                   ttgtaac  putative branch site (score: 2)
                         cctttgccttttgttt  CT-rich tract
             atttgatt  TA-rich tract