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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcacacgattttattctagttcgagcatgcttcacagaaatggctattgtacttgtttactgcatggatcttctacatacatttatgcctaataacagAGTAAAGTCGATGGACGACGCAGTCAGAACCTCAGGTCACTATCATTTGGAAATTCAAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAA

Basic information

species Zea mays
transcript GRMZM5G830874_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G830874_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g08270.3 (Oryza sativa), 3'ss of exon 2
-ttgcacacgattttattctagttcgagcatgcttcacagaaatggctat-tgtact-tgtttactgcatggatcttctacatacatt--tatgcctaataacagAGTAAAGTCGATGGACGACGCAGTCAGAACCTCAGGTCACTATCATTTGGAAATTCAAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAA
 || ||   |    |  |  |    | | |||  | |  || |||  ||  || |   ||| | || || | || |  |  |||   |  ||||   | || |||| |||||| |||||||||  || |||||| || |||||||| || |||||| ||||||||||| ||||||||||||||||||  ||||||||||||| ||
cttccatttggccatgcttga---tgggaatgactaa--gatatgattacatgcatgatgtctgcttcaagcatttatttaatattatcatatgttcattagcagAATAAAGTTGATGGACGATTCAATCAGAATCTGAGGTCACTGTCGTTTGGACATTCAAGTCCTCCATCACCAGCATCATATGGTCAAAATGGTCTTGCAA
















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|194717071|gb|FK934224.1|FK934224
EST:     GAAGCAGGCGCAGCTTAAGCTCGACTATGGATATCATGAATCAGCTGGAG                         AGTAAAGTCGATGGACGACGCAGTCAGAACCTCAGGTCACTATCATTTGGA
genomic: GAAGCAGGCGCAGCTTAAGCTCGACTATGGATATCATGAATCAGCTGGAGgtctgtcctc ... ctaataacagAGTAAAGTCGATGGACGACGCAGTCAGAACCTCAGGTCACTATCATTTGGA
EST: gi|6952374|gb|AW424442.1|AW424442
EST:     GAAGCAGGCGCAGCTTAAGCTCGACTATGGATATCATGAATCAGCTGGAG                         AGTAAAGTCGATGGACGACGCAGTCAGAACCTCAGGTCACTATCATTTGGA
genomic: GAAGCAGGCGCAGCTTAAGCTCGACTATGGATATCATGAATCAGCTGGAGgtctgtcctc ... ctaataacagAGTAAAGTCGATGGACGACGCAGTCAGAACCTCAGGTCACTATCATTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattgtacttgtttactgcatggatcttctacatacatttatgcctaataacagAGTAAAGTCGATGGACGACGCAGTCAGAACCTCAGGTCACTATCATTTGGAAATTCAAGTCCTACATCACCAGCATCATATGCCCAAAATGGTCTTGGAA
                                           gcctaat  putative branch site (score: 3)
                                 atacatttat  TA-rich tract