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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgagttcttctattgtcacaagtttctacttaaaatatggcttgggaattcatcacttatgtttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTCACCTATGCAAAAGAGTTGGTTGAACGGATGGGTCTTGGAAAGTCATCCTCAAATGTTGAACCTC

Basic information

species Zea mays
transcript GRMZM2G023289_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 9
gtaatgagt--tcttctattgtcacaagtttctacttaaaatatggcttggga---attcatcacttatgtttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTCACCTATGCAAAAGAGTTGGTTGAACGGATGGGTCTTGGAAAGTCATCCTCAAATGTTGAACCTC---
|||||  ||  ||||||||  |||||| |||  |  || ||| | | ||||     |||| | |||| | ||||| ||||| ||||||||||| || ||||| ||||||||||||||||||||||||||  | ||||| |||||||| ||||||||   ||||||||||| |||||| |   
gtaatttgttttcttctatcatcacaa-tttgaaaatagaatttagattggtgttcattctttacttgtatttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAA---ATCCTCAAATGCTGAACCCCCAG

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
----------------gtaatgagttcttctattgtcacaagtttctacttaaaatatggcttgggaattcatcact-tatgtt--tttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTCACCTATGCAAAAGAGTTGGTTGAACGGATGGGTCTTGGAAAGTCATCCTCAAATGTTGAACCTC
                   | ||     | |    | |    || | | |  |  |   |  |    ||| | |||  ||      ||||||||||||||||||||| || ||||||||||| ||  | |||||||| || ||| | || | ||| |||||  | || || ||   | |    | ||||||||
gtcttatttttgtctaaccaagaaacgctattccataaatgattacaaatacacctccaggctcaatatttaccacaatacaacgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 9
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------------gtaatgagttcttctattgtcacaagtttctacttaaaatatggcttgggaattcatcactta--tgtttttg------cagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTCACCTATGCAAAAGAGTTGGTTGAACGGATGGGTCTTGGAAAGTCATCCTCAAATGTTGAACCTC
                                ||  | |  |  || |     | || ||   |    ||  ||   |||  | ||| |   ||   || |||        ||||| ||||||||||| || ||||| |||||||| || ||||||||||| |||||||||| | | |||||  | || || |||    | ||   ||| || |
gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 9
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 8
gtaatgagttcttctattgtcacaagtttctacttaaaatatggcttgggaattcatcactt--atgtttt-tgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTCACCTATGCAAAAGAGTTGGTTGAACGGATGGGTCTTGGAAAGTCATCCTCAAATGTTGAACCTC
                         |||| |  ||    |    | ||    |||   ||||  | ||||| | |||||||||||||| || || ||||||||||| || ||||| || ||||||||| | |||   || ||||| || || ||| |   | |   ||  || || |
-------------------------gtttgtgtttttctttcttcctg----ttctatacttcaacgttttctacagGAGGACTTTGGTGGAGGCCATCCGGATCCCAATCTCACGTACGCAAAAGAGCTTGTTTTGCGCATGGGACTGGGGAAGACCGGCCCTCCTGCCGATCCAC

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 9
lower sequence: EFJ09195 (Selaginella moellendorffii), 3'ss of exon 8
gtaatgagttcttctattgtcacaagtttctacttaaaatatggcttgggaattcatcacttatgtttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTCACCTATGCAAAAGAGTTGGTTGAACGGATGGGTCTTGGAAAGTCATCCTCAAATGTTGAACCTC
                         |||| |  ||    |      || |   |  |      | ||| | |||||||||||||| || || ||||||||||| || ||||| || ||||||||| | |||   || ||||| || || ||| |   | |   ||  || || |
-------------------------gtttgtgtttttctttctttctgtgccatacttgaacgt-tttctacagGAGGACTTTGGCGGAGGCCATCCGGATCCCAATCTCACGTACGCAAAAGAGCTTGTTTTGCGCATGGGACTGGGGAAGACCGGCCCTCCTGCCGATCCAC

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|116816329|gb|EC859054.1|EC859054
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCAAAA                         GAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTCACCTATGCAAAAGAG
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCAAAAgtaatgagtt ... gtttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTCACCTATGCAAAAGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacaagtttctacttaaaatatggcttgggaattcatcacttatgtttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTCACCTATGCAAAAGAGTTGGTTGAACGGATGGGTCTTGGAAAGTCATCCTCAAATGTTGAACCTC
                                            tgttttt  CT-rich tract
       tttctacttaaaatat  TA-rich tract