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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCAAGCAGCTTTTACTCTCAAAATATGAACATTGGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTCgtaagtagtaactgcatagtaaagttttatgtttggttctagtactaagtttccagagctaatgcaacatcccctgttgctgattgcag

Basic information

species Zea mays
transcript GRMZM5G825854_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825854_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g34970.1 (Oryza sativa), 5'ss of exon 8
GTATCAAGCAGCTTTTACTCTCAAAATATGAACATTGGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTCgtaagtagtaactgcatagtaaagttttatgtttggttctag--tactaag-tttccagagctaatgcaacatcccctgttgctgattgcag
|| || |  |||||||| ||||||| ||||||||| ||||||||||| ||||||||||| ||||| || || ||||||||||| |||||||||||||  |      || | | | ||| | ||| |||  | || || |||   ||| | ||||   ||||  | | | || ||  ||
GTCTCTACTAGCTTTTATTCTCAAACTATGAACATCGGAAATGAACAATTTCTTCCACTTTTGAAACGGCTCGATGATTGTATTTCgtaagtagtaatag----acaatgctctgtgtgtagttttagggtgctgagatttaaggagttcatgctgtatcctgtttgggtgcttatag

upper sequence: GRMZM5G825854_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA17G04990.1 (Glycine max), 5'ss of exon 8
GTATCAAGCAGCTTTTACTCTCAAAATATGAACATTGGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTCgtaagtagtaac-----tgcatagtaaagttttatg-tttggttct----agtac-taagtttccagagctaatgcaacatcccctgttgctgatt-gcag----------------------------------------------
||  | | ||  ||||| |||| ||| |||||| ||||||||||| | |||||||||||  | || || |||||||| || ||||||| ||||  ||      | |||  ||    ||  |   || ||  |    |||   ||   |  || |    ||  ||| |   || |  ||| || | ||                                              
GTTGCTACCAATTTTTATTCTCCAAACATGAACGTTGGAAATGAAAACTTTCTTCCACTTCTCAAACGACTTGATGAATGCATCTCgtgagtaaaaatccagtttcattctagtacttcgtaactttgtcatgctcagtgtatagaatgtcacaaacgatttaacgttggctttatctgctttgtagttgaacaataaatgtgatcatttacattttttatcttttaatttag
















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|93281267|gb|EB673531.1|EB673531
EST:     GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTC                         GTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTG
genomic: GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTCgtaagtagta ... ctgattgcagGTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTG
EST: gi|22489923|gb|BU049846.1|BU049846
EST:     GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCC-TGATGATTGTATCTC                         GTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTGTTTATTTGGTCAA
genomic: GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTCgtaagtagta ... ctgattgcagGTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTGTTTATTTGGTCAA
EST: gi|211066409|gb|FL073783.1|FL073783
EST:     GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTC                         GTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTGTTTATTTGGTCAA
genomic: GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTCgtaagtagta ... ctgattgcagGTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTGTTTATTTGGTCAA
EST: gi|18450702|gb|BM428980.1|BM428980
EST:     GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTC                         GTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTNGTT-ATTTGGTCA
genomic: GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTCgtaagtagta ... ctgattgcagGTATGTTGAAAACAACCCGCAATATGCTGAATCTGCT-GTTTATTTGGTCA
EST: gi|148952057|gb|EC897846.2|EC897846
EST:     GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTC                         GTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTGTTTATTTGGTCAA
genomic: GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTCgtaagtagta ... ctgattgcagGTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTGTTTATTTGGTCAA
EST: gi|91872014|gb|EB401971.1|EB401971
EST:     GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTC                         GTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTGTTTATTTGGTCAA
genomic: GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTCgtaagtagta ... ctgattgcagGTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTGTTTATTTGGTCAA
EST: gi|87153442|gb|DY398231.1|DY398231
EST:     GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTC                         GTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTGTTTATTTGGTCAA
genomic: GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTCgtaagtagta ... ctgattgcagGTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTGTTTATTTGGTCAA
EST: gi|32859413|gb|CD999094.1|CD999094
EST:     GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTC                         GTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTGTTTATTTGGTCAA
genomic: GGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTCgtaagtagta ... ctgattgcagGTATGTTGAAAACAACCCGCAATATGCTGAATCTGCTGTTTATTTGGTCAA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATCAAGCAGCTTTTACTCTCAAAATATGAACATTGGAAATGAACAGTTTCTTCCACTGTTGAAGCGCCTTGATGATTGTATCTCgtaagtagtaactgcatagtaaagttttatgtttggttctagtactaagtttccagagctaatgcaacatcccctgttgctgattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC