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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCGCTGGGTCCCCGGCGGCGGTTGCGCACAAGATCCAGCTCAAGAGCGCCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacctctcgctctcgctctgccttcttcatgcgatcgattcccccttgttgacgggttgttcgttataattttaagatttttttttctgtcgattgcttctcag

Basic information

species Zea mays
transcript GRMZM2G146012_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146012_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g15260.1 (Oryza sativa), 5'ss of exon 1
GGGCGCTGGGTCCCCGGCGGCGGTTGCGCACAAGATCCAGCTCAAGAGCGCCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacctctcgctctcgctctgccttcttcatgcgatcgattcccccttgttgacgggttgttcgttataattttaagatttttttttctgtcgattgcttctcag-
|    ||||  || | || || |  | ||||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||| || |||||| ||||||  || ||   | | ||| |  || || ||  |    |  |   ||||  ||  ||| ||| ||| | |    |    | |  ||||| |||   ||| ||| |   
GCCTCCTGGCGCCGCCGCCGCCGCGGGGCACAAGATCCAGCTCAAGAGCGCCGACATGAAGGAGGAGATGCGCCAGGAGGCCTTCGACATCGCCCGCGTCgtaaccac-tcgatcccccgcacctccctcctctcgattcccttgttccctgatt--cggattgctcggtttgcgatgtgaaatggtttttgtgttttttggttcgctag
















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|211413157|gb|FL382742.1|FL382742
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211322038|gb|FL425800.1|FL425800
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|50332742|gb|CO527868.1|CO527868
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211328079|gb|FL404916.1|FL404916
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211147695|gb|FL418238.1|FL418238
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|149055663|gb|EE156369.2|EE156369
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211336225|gb|FL371126.1|FL371126
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211254929|gb|FL426613.1|FL426613
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211068885|gb|FL409569.1|FL409569
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GSGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211251155|gb|FL466754.1|FL466754
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211067902|gb|FL369030.1|FL369030
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211453808|gb|FL376129.1|FL376129
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211521197|gb|FL395752.1|FL395752
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|148959413|gb|EE010777.2|EE010777
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|71447723|gb|DR828773.1|DR828773
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211371126|gb|FL382277.1|FL382277
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211479243|gb|FL398888.1|FL398888
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211159719|gb|FL392770.1|FL392770
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211262046|gb|FL417890.1|FL417890
EST:     CCGACATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211206828|gb|FL384241.1|FL384241
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
EST: gi|211294912|gb|FL412765.1|FL412765
EST:     CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATC                         GCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG
genomic: CCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAG

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 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 182

GGGCGCTGGGTCCCCGGCGGCGGTTGCGCACAAGATCCAGCTCAAGAGCGCCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

GGGCGCTGGGTCCCCGGCGGCGGTTGCGCACAAGATCCAGCTCAAGAGCGCCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 76

GGGCGCTGGGTCCCCGGCGGCGGTTGCGCACAAGATCCAGCTCAAGAGCGCCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 69

GGGCGCTGGGTCCCCGGCGGCGGTTGCGCACAAGATCCAGCTCAAGAGCGCCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacct ... tgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCGCTGGGTCCCCGGCGGCGGTTGCGCACAAGATCCAGCTCAAGAGCGCCGATATGAAGGAGGAGATGCGGCAGGACGCCTTCGAAATTGCCCGCATCgtaagaacctctcgctctcgctctgccttcttcatgcgatcgattcccccttgttgacgggttgttcgttataattttaagatttttttttctgtcgattgcttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG