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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttcttttatagtttgaatgcattacacatagtttggctattgaagcttccctttctgcttgttttttattag

Basic information

species Zea mays
transcript GRMZM2G033515_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033515_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 5'ss of exon 5
ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttcttttatagtttgaatgcattacacatagtttggctattgaagcttccctttctgcttgttttttattag----------------------
||||  || ||||||||||||||||  | ||||| |||||||||||||| ||||||||||||||||| ||||| |||||||   |  |   ||   ||  ||  |  ||||| |  |||||| ||||   ||||||||||  ||   ||| |                          
ATGAGGCTCGGGTTAAGGAGTTCAACCTAAAGCAAATGTGGAAGAGCCCCAATGGCACAATTAGGAATATTATCAATGgtatgctggtaccattagtttgatataacacacagaaattggctgttgacatttccctttcttgttacctttgacatttcgctttcgttttacctttcag
















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|67021863|gb|CO450612.1|CO450612
EST:     GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
EST: gi|31353696|gb|CD438053.1|CD438053
EST:     GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
EST: gi|29130361|gb|CB381065.1|CB381065
EST:     GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAG
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAG
EST: gi|84980627|gb|DW530976.1|DW530976
EST:     GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
EST: gi|61119247|gb|DN560208.1|DN560208
EST:     GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGAAACATTATAAATG                         GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
EST: gi|78092177|gb|DV520551.1|DV520551
EST:     GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
EST: gi|211356162|gb|FL188389.1|FL188389
EST:     GAAGCACATGTGGAAGAGCCCAAATCGCACAATTANGAACATTATAARTG                         GTACTGTGTTCAGAGAACCAATTATATG
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATG

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: 39 (upstream exon), 41 (downstream exon)
Score: 19

ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG


Block sizes: 42 (upstream exon), 45 (downstream exon)
Score: 5

ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 19

ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 20

ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttcttttatagtttgaatgcattacacatagtttggctattgaagcttccctttctgcttgttttttattag

- - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - -  GGAAGA