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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcgtgccgtacgtgcgtgcatccaaatgccatgtctgcatgccatgggaaagaagaaaaaaacggccgagttaaagagtttctgacgctgcaaataaaccgtttgatggccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG

Basic information

species Zea mays
transcript GRMZM2G024887_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024887_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g45010.1 (Oryza sativa), 3'ss of exon 1
gtacgtcgtgccgtacgtgcgtgcatccaaatgccatgtctgcatgccatgggaaagaagaaaaaaacggccgagttaaagagtttctgacgctgcaaa------taaaccgtttgatggccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG
         |     |       || ||| ||    | | | | ||   |||||||        ||    |   |||||      ||   ||||||| |      |  |     |  ||   |     |||||||||||||||| ||||||||||| || || ||||||||||||||||| |||||||||||||||||||| ||||||||||||||||| ||| ||||||
---------gtaacgctcaacaaca-ccagattttctttttccctg---tgggaaatcgatcgtaactcacatggttaattgtgatcgcgcgctgcagaggcacgttgattaacttgtgtgggatcttagATGTGCAGCTACTCGTCCATGGACGGCGTCCTCTACTGCAAGACCCACTTTGAGCAGCTCTTCAAGGAGACGGGGAGCTTCTCCAAGAAGTTCGCGCCAG

upper sequence: GRMZM2G024887_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacgtcgtgccgtacgtgcgtgcatccaaatgccatgtctgcatgccatgggaaagaagaaaaaaacggccgagttaaagagtttctgacgctgcaa-ataaaccgtttg---atg-gccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG
                                                   |   |      |   |    |  |||| |   | | |||   |   | || |||  |||    ||| |  |   ||||||| ||| ||| || ||||||||||| ||  ||||||||||||| || || ||||| |||||||||||  | || |  |||  ||| |||||    ||||
---------------------------------------------------gtgcactcattactcattttcttgttagatcttctatgatcatattatatcaacaatttatctatgtgttgatggcagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
















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|211391775|gb|FL355251.1|FL355251
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|211455531|gb|FL349675.1|FL349675
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|21480972|gb|BQ577655.1|BQ577655
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|211378105|gb|FL329996.1|FL329996
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|32869494|gb|CF009176.1|CF009176
EST:     CTACTANT-AGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CTACCA-TAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|32870818|gb|CF010500.1|CF010500
EST:     CCTACCATAAGACATGCTTCAAGGGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|211331555|gb|FL357939.1|FL357939
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|211007496|gb|FL346568.1|FL346568
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|18661649|gb|BM501509.1|BM501509
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|21480781|gb|BQ577464.1|BQ577464
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|211134068|gb|FL308365.1|FL308365
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|211267283|gb|FL319971.1|FL319971
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|26455128|gb|CA826711.1|CA826711
EST:     AGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: AGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|21330893|gb|BQ486274.1|BQ486274
EST:     TACCATAAGACATGCTTCAAGTGCATTCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: TACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|21480794|gb|BQ577477.1|BQ577477
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|116819068|gb|EC862153.1|EC862153
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|32868868|gb|CF008550.1|CF008550
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|21330183|gb|BQ485564.1|BQ485564
EST:     AGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: AGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|9743144|gb|BE519292.1|BE519292
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|32869353|gb|CF009035.1|CF009035
EST:     CCTATTTTTTGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|21330046|gb|BQ485441.1|BQ485441
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|21330759|gb|BQ486140.1|BQ486140
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|32906533|gb|CF011346.1|CF011346
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|211130928|gb|FL366516.1|FL366516
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|211475203|gb|FL333739.1|FL333739
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|50325577|gb|CO520703.1|CO520703
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|21330096|gb|BQ485477.1|BQ485477
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
EST: gi|78109383|gb|DV527799.1|DV527799
EST:     CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCG                         ATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC
genomic: CCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 186

GTGCGACAAGACCGTCCACTTCATCGACCTCCTCACGGCCGACGGCGTCACCTACCATAAGACATGCTTCAAGTGCAGCCACTGCAAAGGGATCCTCTCGgtacgtcgtg ... ccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgagttaaagagtttctgacgctgcaaataaaccgtttgatggccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG
                           aaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtcgtgccgtacgtgcgtgcatccaaatgccatgtctgcatgccatgggaaagaagaaaaaaacggccgagttaaagagtttctgacgctgcaaataaaccgtttgatggccgcctgcagATGTGCAGCTACTCTTCCATGGACGGTGTGCTGTACTGCAAGACCCACTTCGAGCAGCTCTTCAAGGAGACCGGGAGCTTCTCCAAGAACTTCACGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC