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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcaggtactgccttttcatctttccagctgattactgcactcataatatttgtttatgagtgcag

Basic information

species Zea mays
transcript GRMZM2G022909_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022909_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 5
AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcaggtac-tgccttttcatctttccagctgattac-tgcactcataatatt--tgtttatgagtgcag-----------
||||  ||||| || || || ||||| ||  |||| ||||||||||| ||||||||  | || ||||||||||| || || || |||||||| || |||||||| | |  ||  ||    | | |  | |    | ||    || |   ||||  |   | ||| | ||  |             
AAAGCCAAGAAGATTCTTTCTATTCGAGACCGGGGAATTGGTATGACTAAGGAAGACTTAATCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAGgtacgttacttatgtggtgatacgttgtcctgcataatagtatggatcaataaattccatatttctaagatcttgcctttcgcag

upper sequence: GRMZM2G022909_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 5
AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcag----gtactgcct--tttcatctttccagctgattactgcactcataatatttgtttatgagtgcag--------------------------
|| || ||||||||||| || ||||| ||||| ||||| |||||||| ||||| ||| | || |||||| | ||||| || || |||||||| || |||||||  |       | | || ||  | || | ||   |  ||| | ||| | |       ||  |  || | || |                           
AAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAGgtatctttattttgcaatgtctaatatcttgttctgaaatgaattctgaagtttggggtttaatgaattattgaatattaatttatattttcttttatatag
















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|32928361|gb|CF033173.1|CF033173
EST:     GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|29543392|gb|CB603788.1|CB603788
EST:     GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCCCTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|60397681|gb|DN230497.1|DN230497
EST:     GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|60359153|gb|DN226126.1|DN226126
EST:     GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|60352682|gb|DN219655.1|DN219655
EST:     GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|4647087|gb|AI622162.1|AI622162
EST:     TAAGAACCTTGG-ACGATTGCTAAATCTGGCACTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
genomic: TAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|60354666|gb|DN221639.1|DN221639
EST:     GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAG                         GAACATGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|30306649|gb|CD001322.1|CD001322
EST:     GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|32929628|gb|CF034440.1|CF034440
EST:     GGAAGATCTTATTAAGAACCTTGGACCGATTGCTAAATCTGGCACTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|87157046|gb|DY401835.1|DY401835
EST:     GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|60343731|gb|DN210704.1|DN210704
EST:     GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|33091304|gb|CF051298.1|CF051298
EST:     GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|30031912|gb|CB833763.1|CB833763
EST:     GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATAC-
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG
EST: gi|211506092|gb|FL477104.1|FL477104
EST:     GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAG                         GAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATAC-
genomic: GGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG

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), 49 (downstream exon)
Score: 315

AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 303

AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 261

AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 189

AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcagg ... atgagtgcagGAACAGGAGCTGCTCGAGTCTCTTGTCGAAGCTGATACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAATCTGGCACTTCAGgtacttcaggtactgccttttcatctttccagctgattactgcactcataatatttgtttatgagtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC