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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTCCCCTCCCTCCTCCCCGTCGCCAACCAACCTCCAACCCCCAGCCGATCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctctcccgccaccgggctccccgccctcgcttcgctctcaccgtgacccgtttctctccccgcag

Basic information

species Zea mays
transcript GRMZM2G043198_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043198_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g42410.3 (Oryza sativa), 5'ss of exon 1
GCCTCCCCTCCCTCCTCCCCGTCGCCAACCAACCTCCAACCCCCAGCCGATCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgt-cagtgct--ctcccgccaccgggctccccgccc------tcgcttcgctctcaccgtgacccgtttctctccccgcag-------------------------------------------------------------------
 |  | || | | |    ||    ||  ||  ||  |  | | |  |   |  |  |    ||||||||| ||||| ||||||| ||||||||||||||||| | |  |   |||||  | ||      | |  ||      | | ||   | |    || | |  ||    |   ||| |                                                                   
CCGACTCCGCTCACGAGACCTAAACCCTCCTTCCCTCTCCTCTCGTCTCGTTCCCACCACCATGCTGGGCATCGCGAGGAGGCGCCTCGGATCCGGATGCgtacggctcctcctcccctctcctcttctctcatcccgatgattgtttgtttttttttgtaatctcttctcgttttcgcggtttctgattatctgggggtgggggatggatttctgacgctcgccgtcccgtttcgatcgttgtgcag
















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|211444057|gb|FL415432.1|FL415432
EST:     GCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: GCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211273080|gb|FL371948.1|FL371948
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211491514|gb|FL426447.1|FL426447
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCTGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211003333|gb|FL404181.1|FL404181
EST:     DNGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCA-G
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|148930818|gb|EC873192.2|EC873192
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211084499|gb|FL378037.1|FL378037
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|32799489|gb|CD951725.1|CD951725
EST:     GATCCAGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: GATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|148953725|gb|EC899090.2|EC899090
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|32804720|gb|CD956956.1|CD956956
EST:     GATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: GATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|37426139|gb|CF650819.1|CF650819
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|38687965|gb|CK144996.1|CK144996
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|14997073|gb|BI319153.1|BI319153
EST:     CGCGTACGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGATCCCGCCAGG
genomic: CGCGT-CGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|93281968|gb|EB674232.1|EB674232
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCCCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211431560|gb|FL401076.1|FL401076
EST:     GTCGCGCGGAGGCGGCTCGGATCTGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: GTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211311674|gb|FL419261.1|FL419261
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211503999|gb|FL380203.1|FL380203
EST:     GTCGCGCGGAGGCGGCTCGGATCTGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: GTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211056917|gb|FL385087.1|FL385087
EST:     GTCGCGCGGAGGCGGCTCGGATCTGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: GTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211395332|gb|FL395257.1|FL395257
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|8367328|gb|BE050273.1|BE050273
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCTGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211017664|gb|FL418154.1|FL418154
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGGCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211499368|gb|FL394923.1|FL394923
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCTGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211423792|gb|FL402788.1|FL402788
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211063939|gb|FL426137.1|FL426137
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211099620|gb|FL375433.1|FL375433
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211542664|gb|FL412592.1|FL412592
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211054277|gb|FL399886.1|FL399886
EST:     TCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211479962|gb|FL426376.1|FL426376
EST:     GTCGCGCGGAGGCGGCTCGGATCTGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: GTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|31357689|gb|CD442046.1|CD442046
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCTGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211530195|gb|FL395784.1|FL395784
EST:     TMGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211016844|gb|FL388973.1|FL388973
EST:     GTCGCGCGGAGGCGGCTCGGATCTGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
genomic: GTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG
EST: gi|211279267|gb|FL423597.1|FL423597
EST:     TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGC                         GTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGGCAGG
genomic: TCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctc ... ctccccgcagGTGCTCGCCCAGCTGGCGCAGGCCCTCCGCCCCGCCGCCGCTCCCGCCAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTCCCCTCCCTCCTCCCCGTCGCCAACCAACCTCCAACCCCCAGCCGATCGCGTCGGAGATGCTGGGCGTCGCGCGGAGGCGGCTCGGATCCGGATGCgtcagtgctctcccgccaccgggctccccgccctcgcttcgctctcaccgtgacccgtttctctccccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG