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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCCGGTTTTGTAACCCTGAGTTGAGTGAAATAGTCACAAAATGGCTAAAGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggctatatgctaatgcttctaaccttgcttctgcttgtcattactctatccacagtataactgaaaacgttcaacag

Basic information

species Zea mays
transcript GRMZM2G085577_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085577_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g63270.1 (Oryza sativa), 5'ss of exon 10
GCTCCGGTTTTGTAACCCTGAGTTGAGTGAAATAGTCACAAAATGGCTAAAGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtg-gctatatgctaatgcttctaaccttgcttctgcttgtcattactctatccac---agtataactgaaaacgttcaacag
|||||| || || ||||| ||||||||||||||||| ||||||||||||||  |||||||||||||||| || |||||||| || || |||||||| |||||||||| ||    | ||||  |||  | | ||  | ||   | | | |  |||  | ||   |||||||| |||| ||||  ||||
GCTCCGTTTCTGCAACCCAGAGTTGAGTGAAATAGTAACAAAATGGCTAAAAACAGATCAGTGGACAAGCAACCTTGATCTTCTTACCGGACTTCGGAAAgtatgtgtgcatccttctaaaccttgcaccatttttccttgctattactcatctgactacttaagtataaccgaaagcgtt--acag
















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|116826388|gb|EC870170.1|EC870170
EST:     AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAA                         TTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
genomic: AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggct ... cgttcaacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
EST: gi|211057776|gb|FL419530.1|FL419530
EST:     AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAA                         TTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
genomic: AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggct ... cgttcaacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
EST: gi|211327557|gb|FL371056.1|FL371056
EST:     AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAA                         TTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
genomic: AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggct ... cgttcaacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
EST: gi|94480423|gb|EB709381.1|EB709381
EST:     AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAA                         TTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
genomic: AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggct ... cgttcaacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
EST: gi|76924590|gb|DV170029.1|DV170029
EST:     AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAA                         TTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
genomic: AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggct ... cgttcaacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
EST: gi|94472102|gb|EB701060.1|EB701060
EST:     AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAA                         TTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
genomic: AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggct ... cgttcaacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
EST: gi|211319769|gb|FL419318.1|FL419318
EST:     AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAA                         TTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
genomic: AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggct ... cgttcaacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCT
EST: gi|91877192|gb|EB407149.1|EB407149
EST:     AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAA                         TTTGCAGATGATGAAAAGCTTCATGGCTGAGTGGGGCAGCAGCCAA
genomic: AGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggct ... cgttcaacagTTTGCAGATGATGAAAAGCTTCATG-CTGAGTGGG-CAGCAGCCAA

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: 206

GCTCCGGTTTTGTAACCCTGAGTTGAGTGAAATAGTCACAAAATGGCTAAAGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggct ... cgttcaacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCTTGCAAGAAGCGCCTGGCCAAACATGTGTTGGATGTGACAGGTGTTACGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 180

GCTCCGGTTTTGTAACCCTGAGTTGAGTGAAATAGTCACAAAATGGCTAAAGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggct ... cgttcaacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCTTGCAAGAAGCGCCTGGCCAAACATGTGTTGGATGTGACAGGTGTTACGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 61

GCTCCGGTTTTGTAACCCTGAGTTGAGTGAAATAGTCACAAAATGGCTAAAGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggct ... cgttcaacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCTTGCAAGAAGCGCCTGGCCAAACATGTGTTGGATGTGACAGGTGTTACGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 252

GCTCCGGTTTTGTAACCCTGAGTTGAGTGAAATAGTCACAAAATGGCTAAAGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggct ... cgttcaacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCTTGCAAGAAGCGCCTGGCCAAACATGTGTTGGATGTGACAGGTGTTACGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCCGGTTTTGTAACCCTGAGTTGAGTGAAATAGTCACAAAATGGCTAAAGTCAGATCAGTGGACAAGTAATCTTGATCTGCTCACTGGACTTCGCAAAgtatgtggctatatgctaatgcttctaaccttgcttctgcttgtcattactctatccacagtataactgaaaacgttcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA