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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttcaaatcgactgtttgcagcacattattgcagagcatacactaccttgacttggatatataactaaccaaatgaatggatggatggtgaggttcagGAAGCTGTGGGTCTCAAGGGATGAACGGCATGAACGAGAGCAAGCTGGTGGATCTGCTCAACGGCTCCGAGTACGTGCCGACCTACGAGGACAAGGACGG

Basic information

species Zea mays
transcript GRMZM2G138268_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138268_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 3'ss of exon 2
aggttcaaatcgactgt-ttgcagcacattattgcagagcataca-ctaccttgacttggatatataactaaccaaatgaatggatggat-ggtgaggttcagGAAGCTGTGGGTCTCAAGGGATGAACGGCATGAACGAGAGCAAGCTGGTGGATCTGCTCAACGGCTCCGAGTACGTGCCGACCTACGAGGACAAGGACGG
   || || | |  |||  || |  |    |||     ||||  |  |       |||     | |   ||   |  | ||||  || ||   |     ||||||| |||||||||||| ||| ||||||||||||||||||||||| | |  ||||||||||||||||| || || ||||| ||||||||||||||||||||
---tttaattaggttgtactgtataatcaaattaatcggcatggagttgtagatgcttaatgtttttggtatgaagcttaatgtctgaattaattttcatcagGAAACTGTGGGTCTCATGGGGTGAACGGCATGAACGAGAGCAAGATTGCTGATCTGCTCAACGGCTCTGAATATGTGCCAACCTACGAGGACAAGGACGG

upper sequence: GRMZM2G138268_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g43400.1 (Oryza sativa), 3'ss of exon 2
--aggttcaaatcgactgtttgcagcacattattgcagagcatacactaccttgacttggatatataactaaccaaatgaatggatggatggtgaggttcagGAAGCTGTGGGTCTCAAGGGATGAACGGCATGAACGAGAGCAAGCTGGTGGATCTGCTCAACGGCTCCGAGTACGTGCCGACCTACGAGGACAAGGACGG------------
  |      ||     | | |  || || | |||  |      | |  | ||        | || |    ||   |||     | | | || | | ||||||| |  |||||||| ||     | | | || |||| ||||||||        | |||    | | |   |||||||||||||| |||||||||||||||||            
tcaaagatgaacgatatatatatag-ac-tgattaaaatattaagagaaactattgcaaaacatctgttaaaattaatagggtggttgttgatcatgttcagGCAAGTGTGGGTCCCA-----TCAGCAGC-TGAAGGAGAGCAAT------AAGCTGAGAGATGACCTGGAGTACGTGCCGACGTACGAGGACAAGGACGGCGACTGGATGCT

upper sequence: GRMZM2G138268_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G23050.2 (Arabidopsis thaliana), 3'ss of exon 2
aggttcaaatcgactgtttgcagcacattattgcagagcatacactaccttgacttggatatataa-ctaaccaaatgaatggatggatggtgaggttc--agGAAGCTGTGGGTCTCAAGGGATGAACGG---CATGAACGAGAGCAAGCTGGTGGATCTGCTCAACGGCTCCGAGTACGTGCCGACCTACGAGGACAAGGACGG
  | |       | ||| | || |  |    || |    ||| | |||    |    || | ||||  | |    ||   || |||  | |      |   ||||| || |||  | ||||| ||||  |    ||||||||||||||||||  || ||||||| ||  |||| ||||| ||||| | |||||||||||| ||   
--gattttgctaaatgtatacaacttaaatatgtattatatatattacac-aataatgacacataaatttatatgatttttgaatgtcttgaatatcttcaagGAAACTATGGAGCACAAGGAATGATAGATTTCATGAACGAGAGCAAGCTAATGAATCTGCTGAATAGCTCTGAGTATGTGCCAAGCTACGAGGACAAAGA---

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|71760821|gb|DR958758.1|DR958758
EST:     CCAGCAGCTGTCCAAGGCGCTCGAGAACATGTTCAGCTCCTTCACCATCG                         GAAGCTGTGGGTCTCAAGGGATGAACGGCATGAACGAGAGCAAGCTGGTGG
genomic: CCAGCAGCTGTCCAAGGCGCTCGAGAACATGTTCAGCTCCTTCACCATCGgtactaaatt ... tgaggttcagGAAGCTGTGGGTCTCAAGGGATGAACGGCATGAACGAGAGCAAGCTGGTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccttgacttggatatataactaaccaaatgaatggatggatggtgaggttcagGAAGCTGTGGGTCTCAAGGGATGAACGGCATGAACGAGAGCAAGCTGGTGGATCTGCTCAACGGCTCCGAGTACGTGCCGACCTACGAGGACAAGGACGG
                   aactaac  putative branch site (score: 1)
             atatataactaa  TA-rich tract