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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagtttgtttaagtattttgagtttgatgcaaagggtgtgcttgtatcacaagattcttatgaattttgtcgaaatcaaggtcatgccatgttattctacctgtacctgtaactttgttgttctatattactcagatgtaacccaatgttttgcag

Basic information

species Zea mays
transcript GRMZM2G432128_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G432128_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 5'ss of exon 3
CATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagtttgtttaagtattttgagtttgatgcaaagggtgtg-cttgt-atcacaagattcttatgaattttgtcgaaatcaaggtcatgccatgttattctacctgtacctgtaactttgttgttctatattactcagatgtaacccaatgttttgcag
||||| |||| |||||||| ||||||||||| |||||  | || |||||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||   ||  | |  |||||| |  |   ||| |||        |||| ||||||   || | ||  ||||    | |||  || |  ||   |||   |||                                                          
CATTTTTGGATCTGGACATTAAGTACTATGACTTGGGAGTTCTCCACCGTGATGCAACTGATGACAAGGTCACCGTGGAGGCTGCAGAGGCTACTCTCAAgtaaggaatt--taagatattttaaagtccgtgctaagaagacaatttgtgatcacactgttttcattgatttgtgtggaatttagtt--tggtgtgtccatct----------------------------------------------------------
















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|148957374|gb|EC903424.2|EC903424
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211301308|gb|FL411053.1|FL411053
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211348619|gb|FL403648.1|FL403648
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211317120|gb|FL381346.1|FL381346
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211202503|gb|FL419113.1|FL419113
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211332798|gb|FL423282.1|FL423282
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|149110655|gb|EE190535.2|EE190535
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211245761|gb|FL421854.1|FL421854
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211158137|gb|FL392765.1|FL392765
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|33101480|gb|CF061440.1|CF061440
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|31612230|gb|CD568852.1|CD568852
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|67031198|gb|CO459947.1|CO459947
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACTACGCGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211531114|gb|FL426904.1|FL426904
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|149031177|gb|EE286335.2|EE286335
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211264490|gb|FL417909.1|FL417909
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211003472|gb|FL408513.1|FL408513
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|29130876|gb|CB381580.1|CB381580
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211097134|gb|FL375411.1|FL375411
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|31356012|gb|CD440369.1|CD440369
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|74237580|gb|DT645494.1|DT645494
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|148937601|gb|EC881791.2|EC881791
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|76286556|gb|DV026124.1|DV026124
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211516468|gb|FL412101.1|FL412101
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211414079|gb|FL428571.1|FL428571
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211365953|gb|FL391119.1|FL391119
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211113009|gb|FL402637.1|FL402637
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|148961311|gb|EE012038.2|EE012038
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|149055178|gb|EE156095.2|EE156095
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211392274|gb|FL373436.1|FL373436
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211500096|gb|FL423896.1|FL423896
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|50338700|gb|CO533826.1|CO533826
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211214727|gb|FL396531.1|FL396531
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|18659665|gb|BM500459.1|BM500459
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
EST: gi|211352901|gb|FL376492.1|FL376492
EST:     GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAA                         GTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG
genomic: GAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG

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), 45 (downstream exon)
Score: 189

CATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 664

CATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 690

CATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 634

CATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagttt ... tgttttgcagGTACAACGTGGCTATTAAGTGTGCGACCATTACTCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTTCTGGACCTGGACATCAAGTACTATGATTTGGGGATACTGCACCGTGAAGCAACTGATGACAAGGTCACAGTGGAGGCTGCAGAGGCTACTCTCAAgtaagagtttgtttaagtattttgagtttgatgcaaagggtgtgcttgtatcacaagattcttatgaattttgtcgaaatcaaggtcatgccatgttattctacctgtacctgtaactttgttgttctatattactcagatgtaacccaatgttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG