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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTGTCGTTAAAGCCAAATCACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccactttctagtcgatgtcgattagaaccaatgcataatatgtcttggaacactactgaatttttatatgctacatatgctatggtgaaagtacg...

Basic information

species Zea mays
transcript GRMZM2G047093_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047093_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g43030.1 (Oryza sativa), 5'ss of exon 5
TGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTGTCGTTAAAGCCAAATCACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccactttctagtcgatgtcgattagaaccaatgcataatatgtcttg-gaacactactgaatttttatatgcta-catatgctatggtgaaagtacg
||||||||||||||||||||||||||||||||||  |  | ||||||||||||||||||||||||||||||||||| || ||||| ||||| | ||| |||||||| |  || |  ||  |||    ||    || |  |  |||| | ||| | ||   |||   |     |||  || || ||   | |       |  |
TGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTAACACTGAAGCCAAATCACCGCATGAACTGGATTGGTTTTGCTGTAGCTCACCATTTAAGTTCCAAgtatgctaacttattttc--tgttagatattgtcattaaaatatattttttgagtacttgacttgctcagactatcttatcaaatctgaggcctgtcatgag
















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|32930286|gb|CF035098.1|CF035098
EST:     CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
EST: gi|18384963|gb|BM418162.1|BM418162
EST:     CACCGCATGAACTGGATTGGTTTTGCGGNTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
EST: gi|211307138|gb|FL392844.1|FL392844
EST:     CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAGTAGAAGTATTG
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTG
EST: gi|18383999|gb|BM417199.1|BM417199
EST:     CACCGCATGAACTGGATTGGTTTTGCGGNTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
EST: gi|211351633|gb|FL428915.1|FL428915
EST:     ACCGCATGAACTGGATTGGTTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGG
genomic: ACCGCATGAACTGGATTGGTTTT-GCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGG
EST: gi|18654934|gb|BM499739.1|BM499739
EST:     CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
EST: gi|76013182|gb|DT940352.1|DT940352
EST:     CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
EST: gi|18963330|gb|BM660374.1|BM660374
EST:     CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
EST: gi|32933101|gb|CF037913.1|CF037913
EST:     CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
EST: gi|32943122|gb|CF047941.1|CF047941
EST:     CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
EST: gi|18661955|gb|BM501667.1|BM501667
EST:     CACCGCATGAACTGGATTGGTTTTGCGGNTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
EST: gi|211339025|gb|FL403590.1|FL403590
EST:     ACCGCATGAACTGGATTGGGTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCA
genomic: ACCGCATGAACTGGATTGG-TTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCA
EST: gi|19855106|gb|BQ060158.1|BQ060158
EST:     CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
EST: gi|211184480|gb|FL377621.1|FL377621
EST:     CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAG
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAG
EST: gi|211223503|gb|FL389609.1|FL389609
EST:     ACCGCATGAACTGGATTGGTTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAG
genomic: ACCGCATGAACTGGATTGGTTTT-GCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAG
EST: gi|33095320|gb|CF055314.1|CF055314
EST:     CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAA                         TTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA
genomic: CACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGA

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: 261

TGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTGTCGTTAAAGCCAAATCACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGATGATTATCCTCCAGAGAATGAGCGATATGAACACAATGAAATGCTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

TGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTGTCGTTAAAGCCAAATCACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGATGATTATCCTCCAGAGAATGAGCGATATGAACACAATGAAATGCTGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 229

TGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTGTCGTTAAAGCCAAATCACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGATGATTATCCTCCAGAGAATGAGCGATATGAACACAATGAAATGCTGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 160

TGTCTGGCTTTGTTGAGACTAGGCAACAACTTTTGTCGTTAAAGCCAAATCACCGCATGAACTGGATTGGTTTTGCGGTTGCTCATCATTTGAATTCTAAgtatgccact ... tcacttgcagTTCTTCCAAGGCAGTAGAAGTATTGGAGGCATACGAGGGAACACTGGAAGATGATTATCCTCCAGAGAATGAGCGATATGAACACAATGAAATGCTGCTG