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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatatgttgggcatttggtgaagatgtgaaaagcgtgctcgtttttcctttttaactttgacctaaaattcatttgcttcaataccatattaccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATATCGCTTGGTTTACTCCCGTGGAGCTCTTTAAG

Basic information

species Zea mays
transcript GRMZM2G101217_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101217_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g68390.1 (Oryza sativa), 3'ss of exon 2
gatatgttgggcatttggtgaagatgtgaaaagcgtgctcgt---ttttcctttttaactttgacctaaaattcatttgcttcaataccatattacc-atgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATATCGCTTGGTTTACTCCCGTGGAGCTCTTTAAG
    |||||  | |    |||   | ||  ||    | |  |   || | || ||| | | |     | | || | | |   |   |  |  || |  ||||||| |||||||| ||||| ||| ||||||||||| |||| ||||||||||| ||||||||||| ||||| ||||||||||| |||
---ctgttgaac-tccattgattgtttgccaattacgattctgtgttgtgctgttttaatatcttggatatttgactagaaacggaagtaatttgcttatgtagGTAGGAGTGCGTATATGCAGTACCTTGATAAGTTGTACAAGAAGCATGACATCGCTTGGTTCACTCCAGTGGAGCTCTTCAAG
















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|211531113|gb|FL426903.1|FL426903
EST:     GGGGCCGGTGGGCGTTCTTGACGC-AGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211153475|gb|FL406036.1|FL406036
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211057983|gb|FL426573.1|FL426573
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211269212|gb|FL410574.1|FL410574
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|76924073|gb|DV169790.1|DV169790
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|93012306|gb|EB637826.1|EB637826
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|71312573|gb|DR792811.1|DR792811
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|50325602|gb|CO520728.1|CO520728
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211209580|gb|FL394645.1|FL394645
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|89250708|gb|DY622494.1|DY622494
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTTGATAAGCTGTATAAGAAGCATGAT
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTT-GATAAGCTGTATAAGAAGCATGAT
EST: gi|211491486|gb|FL425979.1|FL425979
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|37417541|gb|CF646424.1|CF646424
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|93012540|gb|EB638060.1|EB638060
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211063350|gb|FL405207.1|FL405207
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|101391071|gb|EB817469.1|EB817469
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211197467|gb|FL425782.1|FL425782
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211511752|gb|FL412067.1|FL412067
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATA
EST: gi|211164475|gb|FL391064.1|FL391064
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGANGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211428747|gb|FL388358.1|FL388358
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATR
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGAT-
EST: gi|211524044|gb|FL387968.1|FL387968
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211079207|gb|FL387329.1|FL387329
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|76281532|gb|DV021100.1|DV021100
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|148959299|gb|EE010710.2|EE010710
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211209713|gb|FL401773.1|FL401773
EST:     GGGGCCGGTGGGCGTTCTTGACGC-AGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGANGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211054342|gb|FL401189.1|FL401189
EST:     GGGGCCGGTGGGCGTTCTTGACGC-AGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211428657|gb|FL384948.1|FL384948
EST:     GGCCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGGATAAGAAGCATGAT
genomic: GACC-GGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGA-GGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGAT
EST: gi|211463727|gb|FL386698.1|FL386698
EST:     GGGGCCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|148960597|gb|EE011219.2|EE011219
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|211085712|gb|FL420035.1|FL420035
EST:     GGGGCCGGTGGGCGTTCTTGACG-CAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|71418854|gb|DR804568.1|DR804568
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|50337135|gb|CO532261.1|CO532261
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|71327533|gb|DR800378.1|DR800378
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|50336106|gb|CO531232.1|CO531232
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
EST: gi|71303088|gb|DR787655.1|DR787655
EST:     GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGG                         GGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA
genomic: GGGACCGGTGGGCGTTCTTGACGCCAGCATCCGCTTCAACCAGCTCGAGGgtggtctcct ... taccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttttaactttgacctaaaattcatttgcttcaataccatattaccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATATCGCTTGGTTTACTCCCGTGGAGCTCTTTAAG
                  taaaattcattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatatgttgggcatttggtgaagatgtgaaaagcgtgctcgtttttcctttttaactttgacctaaaattcatttgcttcaataccatattaccatgtagGGAGGAGTGCATATATACAGCACCTTGATAAGCTGTATAAGAAGCATGATATCGCTTGGTTTACTCCCGTGGAGCTCTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT