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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACATGTTGGGTCGATTTCGGAAAGCAGTTAAATGGGCATCACTTTTTTCACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcctactatattttgtttcactttctctcaactgtattttaatagtatttgaactattttgaagatcaatctaaaatattttcaccaaaacacaattttttctcag

Basic information

species Zea mays
transcript GRMZM2G121022_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121022_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g23360.1 (Oryza sativa), 5'ss of exon 4
CTACATGTTGGGTCGATTTCGGAAAGCAGTTAAATGGGCATCACTTTTTTCACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcctactatattttgtttcactttctctcaactgtattttaatagtatttgaactattttga-agatcaatctaaaatattttca---ccaaaacacaattttttctcag-----------------
||||||||| ||| ||||| | ||||| || ||||||||| | ||||||||||| ||||||||| ||||||||||||||||||| ||| | ||||||||||| |||||| |||    |||| |||   |||     ||||  | |  |  | | ||      || |||  | || |    | ||   || ||   | || |   |||  |||||  |                 
CTACATGTTAGGTAGATTTAGAAAAGCTGTCAAATGGGCAACGCTTTTTTCACATTTATGTTCTCTAAAAGGAGATTCCAGGACGTCTTTGGAAGCTGAGgtgtgtttcatacccccttttttttttttttgagaaaactcaaatcaagaaattttaaggtgatattgccatatgagaaaataacccttacaatactaacattaaataatttctttgataaaattgttttgcag

upper sequence: GRMZM2G121022_T04 (Zea mays), 5'ss of exon 3
lower sequence: AT5G61970.1 (Arabidopsis thaliana), 5'ss of exon 5
CTACATGTTGGGTCGATTTCGGAAAGCAGTTAAATGGGCATCACTTTTTTCACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcctactatattttgtttcactttctctcaactgtattttaatagtatttgaactattttgaagatcaatctaaaatattttcaccaaaacacaattttttctcag----------------------------------------------------------------------------
 ||  || | ||| |  |  |||| |||||||||||||| || ||||| |||   || || ||| | ||   |||||||||||||||||| |||||||||||||  ||   ||   |  | ||| || | | ||  || | ||  |  |||  || |  |||  ||||||    |    | ||||  |          |   ||||  || ||                                                                            
ATATTTGGTTGGTAGGCTGAGGAAGGCAGTTAAATGGGCTTCCCTTTTCTCAAGTTTGTGCTCTATTAAGACAGATTCCAGGACATCTCTGGAAGCTGAGgtattcttgtgacctcaggt-gttgcagtat-tcataaatttacat--ataacatattcactgctttgaaaggaagaagagaatacctcagttt---taggcttttagcttagttgtttcatgtaatacgggtgtttactctataaatgcttgacatgagtcgtcatattttatcttactgttttatag
















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|47962062|gb|CN844771.1|CN844771
EST:     ACAATTATGTTCTGTAAAAGGAGATTCCAGGNACATCTCTAGAAGCTGAG                         GCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
genomic: ACAATTATGTTCTGTAAAAGGAGATTCCAGG-ACATCTCTAGAAGCTGAGgtatgtttcc ... tttttctcagGCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
EST: gi|148975996|gb|EE025851.2|EE025851
EST:     CACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAG                         GCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
genomic: CACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcc ... tttttctcagGCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
EST: gi|149106635|gb|EE188528.2|EE188528
EST:     CACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAG                         GCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
genomic: CACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcc ... tttttctcagGCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
EST: gi|211260538|gb|FL346342.1|FL346342
EST:     CACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAG                         GCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
genomic: CACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcc ... tttttctcagGCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
EST: gi|76286956|gb|DV026524.1|DV026524
EST:     CACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAG                         GCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
genomic: CACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcc ... tttttctcagGCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
EST: gi|51592489|gb|CV071635.1|CV071635
EST:     ACAATTATGTTCTGTAAAAGGAGATTCCAAGGACATCTCTAGAAGCTGAG                         GCATATGCTTCATATATGAAGGGTGCTTTG
genomic: ACAATTATGTTCTGTAAAAGGAGATTCCA-GGACATCTCTAGAAGCTGAGgtatgtttcc ... tttttctcagGCATATGCTTCATATATGAAGGGTGCTTTG
EST: gi|67026820|gb|CO455569.1|CO455569
EST:     CACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAG                         GCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
genomic: CACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcc ... tttttctcagGCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
EST: gi|31358954|gb|CD443311.1|CD443311
EST:     CACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAG                         GCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT
genomic: CACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcc ... tttttctcagGCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 327

CTACATGTTGGGTCGATTTCGGAAAGCAGTTAAATGGGCATCACTTTTTTCACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcc ... tttttctcagGCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAATATAGATGCCGCAATGATAAATTTCAAGAATACGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 189

CTACATGTTGGGTCGATTTCGGAAAGCAGTTAAATGGGCATCACTTTTTTCACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcc ... tttttctcagGCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAATATAGATGCCGCAATGATAAATTTCAAGAATACGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 138

CTACATGTTGGGTCGATTTCGGAAAGCAGTTAAATGGGCATCACTTTTTTCACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcc ... tttttctcagGCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAATATAGATGCCGCAATGATAAATTTCAAGAATACGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 347

CTACATGTTGGGTCGATTTCGGAAAGCAGTTAAATGGGCATCACTTTTTTCACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcc ... tttttctcagGCATATGCTTCATATATGAAGGGTGCTTTGTTTTTTGAGCAAGACAAGAATATAGATGCCGCAATGATAAATTTCAAGAATACGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACATGTTGGGTCGATTTCGGAAAGCAGTTAAATGGGCATCACTTTTTTCACAATTATGTTCTGTAAAAGGAGATTCCAGGACATCTCTAGAAGCTGAGgtatgtttcctactatattttgtttcactttctctcaactgtattttaatagtatttgaactattttgaagatcaatctaaaatattttcaccaaaacacaattttttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA