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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgctgtgattcaatctgggctttgttgtcacctgtcataaaaactaagcattgatgttgtcttatcagatatatctattgttgggaagtgtttg...

Basic information

species Zea mays
transcript GRMZM2G146472_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146472_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g06760.2 (Oryza sativa), 5'ss of exon 2
GAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgac----gtgctgtgattcaatctgggctttgttgtcacctgtcataaaaactaagcattgatgttgtcttatcagatatatctattgttgggaagtgtttg
||||||||| ||||| || ||||| ||  ||||||||||||| |||||| | ||||||||||||||||||||||||||||||||||||||| |||||||||||||     | || | | |     | |||| |||||| |  ||   || ||   | |||   |  || | || |   || | |  |   ||   |        
GAAGCCTCGCAATGAGACACCAATTAGTGAGAATGAGATCAGGATCACTGCACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctactactattactttcctttggctatgttgttatttgaggtagaa--catgcagcaacctt-ttttgtgccatgttttaacaattaacag-------

upper sequence: GRMZM2G146472_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g06760.1 (Oryza sativa), 5'ss of exon 2
GAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacg----tgctgtgattcaatctgggctttgttgtcacctgtcataaaaactaagcattgatgttgtct-tatca-gatatatctattgttgggaagtgtttg
||||||||| ||||| || ||||| ||  ||||||||||||| |||||| | ||||||||||||||||||||||||||||||||||||||| |||||||||||||     | || | | |     | |||| |||||| |  ||   || ||   | |||   |  || | | |  || | | || | |||    ||| | |    
GAAGCCTCGCAATGAGACACCAATTAGTGAGAATGAGATCAGGATCACTGCACAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGTTGCTTGAGgtgaccctactactattactttcctttggctatgttgttatttgaggtagaa--catgcagcaaccttttttgtgccatgttttaacaattaacaggacgcg----
















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|89248294|gb|DY620080.1|DY620080
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211179477|gb|FL252804.1|FL252804
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211062369|gb|FL252799.1|FL252799
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211062365|gb|FL252795.1|FL252795
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211179476|gb|FL252803.1|FL252803
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211059403|gb|FL252784.1|FL252784
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211062364|gb|FL252794.1|FL252794
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211062361|gb|FL252791.1|FL252791
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|149078577|gb|EE167361.2|EE167361
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211062368|gb|FL252798.1|FL252798
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|149109057|gb|EE189984.2|EE189984
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211062371|gb|FL252801.1|FL252801
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211062360|gb|FL252790.1|FL252790
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211062359|gb|FL252789.1|FL252789
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATRTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211062367|gb|FL252797.1|FL252797
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211179475|gb|FL252802.1|FL252802
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211062362|gb|FL252792.1|FL252792
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211059404|gb|FL252785.1|FL252785
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|29945425|gb|CB815632.1|CB815632
EST:     CTCAGGGGAGGAAGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211062366|gb|FL252796.1|FL252796
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
EST: gi|211059402|gb|FL252783.1|FL252783
EST:     CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAG                         GAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT
genomic: CTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAAT

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: 49 (upstream exon), 48 (downstream exon)
Score: 467

GAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 696

GAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 492

GAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 270

GAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgct ... acttttacagGAAAATGGACATGATGAGATTAGTATCAAGGCCATGGGACGGGCCATAAATAAGACAGTTATGGTTGTTGAATTGATCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCCTCGGAATGACACGCCAATCAGCCAGAATGAGATCAGAATCACTACTCAGGGGAGGATGAGGAACTATATCAGCTATGGGATGTCGCTGCTTGAGgtgacgtgctgtgattcaatctgggctttgttgtcacctgtcataaaaactaagcattgatgttgtcttatcagatatatctattgttgggaagtgtttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaacta