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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTTTCCTCTGACATGGAGGCCCTTCACGACAAGGTTAAGAAGCAAATCATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacggcgtaggtggttcggaccatatgctcatgctccggatgtcgaattttaggatgagctaatatgctgtgcctgcctgtcctgtttcttattc...

Basic information

species Zea mays
transcript GRMZM2G133624_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133624_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g05090.1 (Oryza sativa), 5'ss of exon 2
GTGGTTTCCTCTGACATGGAGGCCCTTCACGACAAGGTTAAGAAGCAAATCATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacggcgtaggtggttcggaccatatgctcatgctccggatgtcgaattttaggatgagc-taatatgctgtgcctgcctgtcctgtttcttattc--------------------
|||||| ||||||| ||||| | |||| | || || || || |||||| ||||||| ||||||||||||| ||||||    | ||| || || ||||||||| |||| | | || || || | |    | | |   ||||  ||||   ||   |||| |||||  ||||||  | | ||||  | | |   || || ||                     
GTGGTTACCTCTGATATGGAAGTCCTTAATGATAAAGTCAAAAAGCAAGTCATCAAGGAAGGCCATGGCAAGAAACCCTCAAGGTTTGCCACATGCTTTGgtaagtatgccataagtagt-cagtttgt-tccatttgcttaggattgtga---ttagaatgaggataatatattatacctgattttgcaaattatttttttcccaatctttgtcttgcag
















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|211436147|gb|FL367592.1|FL367592
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|76918516|gb|DV167329.1|DV167329
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|71765927|gb|DR963864.1|DR963864
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|71438300|gb|DR819350.1|DR819350
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|71435151|gb|DR816201.1|DR816201
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|32864226|gb|CF003908.1|CF003908
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|211189090|gb|FL366153.1|FL366153
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|211050008|gb|FL347973.1|FL347973
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|211270715|gb|FL364943.1|FL364943
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|78089641|gb|DV518015.1|DV518015
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|211133426|gb|FL346177.1|FL346177
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|211320437|gb|FL345942.1|FL345942
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTAYAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|71306393|gb|DR789338.1|DR789338
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|211078378|gb|FL344979.1|FL344979
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|149015212|gb|EE044997.2|EE044997
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|71299221|gb|DR785609.1|DR785609
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|78108738|gb|DV527155.1|DV527155
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|149076434|gb|EE165057.2|EE165057
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|211036126|gb|FL344517.1|FL344517
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|211257634|gb|FL327800.1|FL327800
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|211491420|gb|FL310086.1|FL310086
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|76021436|gb|DT948606.1|DT948606
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|211257312|gb|FL311217.1|FL311217
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|211274567|gb|FL349919.1|FL349919
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|211465020|gb|FL331108.1|FL331108
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|71435313|gb|DR816363.1|DR816363
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|9794264|gb|BE552572.1|BE552572
EST:     CATTTTATAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
EST: gi|71321226|gb|DR797322.1|DR797322
EST:     CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTG                         TGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT
genomic: CATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCT

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: 231

GTGGTTTCCTCTGACATGGAGGCCCTTCACGACAAGGTTAAGAAGCAAATCATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

GTGGTTTCCTCTGACATGGAGGCCCTTCACGACAAGGTTAAGAAGCAAATCATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 119

GTGGTTTCCTCTGACATGGAGGCCCTTCACGACAAGGTTAAGAAGCAAATCATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

GTGGTTTCCTCTGACATGGAGGCCCTTCACGACAAGGTTAAGAAGCAAATCATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacgg ... ggtgttgcagTGCACTATAGAGCATGGGTTCAAGGATCATCGCATAAATTTGAGGATACCTGGCAAGAGCAACATCCAATTGAACTAGTACTTGGAAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTTTCCTCTGACATGGAGGCCCTTCACGACAAGGTTAAGAAGCAAATCATCAAAGAAGGCCATGGCAGGAAACCGCTGAAGTTCGCGACGTGCTTTGgtgagtacggcgtaggtggttcggaccatatgctcatgctccggatgtcgaattttaggatgagctaatatgctgtgcctgcctgtcctgtttcttattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG