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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcgtagacaagacttctttaattgcttttctgtaacagtggttactaaataaacatgttattctttgactgttacagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA

Basic information

species Zea mays
transcript GRMZM2G091119_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 5
gtcgtagacaagacttctttaattgcttttct-----gtaacagtggttactaaataaacatgttattctttgactgtta-cagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA
||  | |||||   ||||||     ||  | |     |||      |  | |   | |||||| | ||  |||  ||| |  |||||| ||||||||| |||||||| ||||| ||||| || ||||| ||||||||||||||||||||||| ||||||||| | ||||| |||||||| ||||
gtt-tggacaaagtttctttgtactctactgtagttagtagggaaagacagttccttaacatgatgtttattgggtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAGGAAGTTCTCACTGATGCGTGCTGGGCTCTTTCATATTTATCTGATGGCA

upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 5
------------gtcgtagacaagacttctttaattgctttt---ctgtaacagtg----gttactaaataaacatgttattctttgactgttac---agACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA
            ||    | |  |  ||   | |||  || |   |||  |  |||     || |  | |  | |  |||| |||||  | || |   ||  ||| ||||| || || || ||||| || ||||||||||| |||||||| |||||| | |||||||| || |||||  |||||||  | ||||| || |
cattggtcttttgtttatgtcctgcttttactgatttattataagctgctattgtgttttatttcacagttcatacattatactttgtttttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAAGAAGTTTTGACTGATGCATGTTGGGCACTGTCATATCTTTCTGATGGTA

upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT4G02150.1 (Arabidopsis thaliana), 3'ss of exon 5
--gtcgtagacaagacttctttaattgcttttctgtaacagtggttactaaata---aacatgttattctttga----ctgtt---acagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA
   || |  |  | ||    || ||||  | ||   || | |  |||  |        | || || ||  || |     | ||    |||||  | || ||| | ||||  ||||  || ||| | || || |  ||||| ||||||||||| ||||| ||||||||| |||||||| | || ||     
gtttccttaaatatacacactttattgaatctccacaatattttttaacatgcttctgatattttgttacttaaaacatttttcgagcagACACAACCAGCTTTACCAGTTCTTGAGCGCCTTGTGCAATCAATGGATGAAGAAGTTCTCACAGATGCATGCTGGGCTCTGTCATACCTCTCGGATAATT

upper sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ31557 (Selaginella moellendorffii), 3'ss of exon 5
gtcgtagacaagacttctttaattgcttttctgtaacagtggttactaaataaacatgttattctttgactgttacagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA
   |||     | | | | ||      |   |  ||   || |   |         |||| ||  |||       ||| | |  |||||| |  | || || | |   || || ||||| |  || || ||||| || |||||||| |||||||||||||||||| |||| || || |
---gtatgtgggtcatttgtaggcatgtcgatacaaatttgatcgttggtcg---gtgttgtttcttg-------cagTCGAGACCTGCTTTATCTGCTCTAGAAAAGCTGATTCATTCGACTGACGAAGAAGTCCTTACTGATGCATGCTGGGCTTTGTCATACATATCCGATGGTA

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|211099873|gb|FL161944.1|FL161944
EST:     GGACTCTTTCCAACTTTTGCAGGGGAAAGCCACAGCCATCATTTGATCAG                         ACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAG
genomic: GGACTCTGTCCAACTTTTGCAGGGGAAAGCCACAGCCATCATTTGATCAGgtcgtagaca ... actgttacagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAG
EST: gi|211094922|gb|FL161920.1|FL161920
EST:     GGACTCTTTCCAACTTTTGCAGGGGAAAGCCACAGCCATCATTTGATCAG                         ACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCANCGATGAG
genomic: GGACTCTGTCCAACTTTTGCAGGGGAAAGCCACAGCCATCATTTGATCAGgtcgtagaca ... actgttacagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttttctgtaacagtggttactaaataaacatgttattctttgactgttacagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGATGAGGAAGTTCTCACTGATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCA
                   ttactaaataaacatg  TA-rich tract