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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCTCTATTAGCAGCTGAATCACGGGCTGAGAAAGCAAAGAAAGGAGTGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgatattcatttattccatcagttcgattttgatattctctgcgtcatcattaacctatcagtgtggtccttatatggatag

Basic information

species Zea mays
transcript GRMZM2G136296_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136296_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 5'ss of exon 10
TGATGCTCTATTAGCAGCTGAATCACGGGCTGAGAAAGCAAAGAAAGGAGTGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgatattcatttattccatcagttcgattttgatattctctgcgtcatcattaacctatcagtgtggtccttatatggatag
|||    || || || ||||||||||| ||||||||||||||||||||||| ||||||  ||||||||| ||||| ||||| |||||||| || ||||| ||  |  |   |   || |||  | | ||  | |||       |  ||  | | ||||||        || || | |||  |   ||
TGACCTGCTGTTGGCGGCTGAATCACGAGCTGAGAAAGCAAAGAAAGGAGTTCATTCTGCAAAAGAATCACCTGTCATGCACATAACAGACTTGACAACGgtttggcactcttgcttgttcttttacttttactttt---cctttggcacctttattaactc------gtagttcctatgcgctcag
















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|211385597|gb|FL201909.1|FL201909
EST:     TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACT                         GTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
genomic: TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgata ... atatggatagGTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
EST: gi|32841124|gb|CD980805.1|CD980805
EST:     TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACT                         GTATCTGCAAACAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
genomic: TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgata ... atatggatagGTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
EST: gi|32932038|gb|CF036850.1|CF036850
EST:     TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACT                         GTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
genomic: TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgata ... atatggatagGTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
EST: gi|67040223|gb|CO466478.1|CO466478
EST:     TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACT                         GTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
genomic: TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgata ... atatggatagGTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
EST: gi|211388222|gb|FL201915.1|FL201915
EST:     TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACT                         GTATCTGCAAAGAAGGCCAAAGATTNCCTTCCCTTCTTGCAGAGGAACAGA
genomic: TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgata ... atatggatagGTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
EST: gi|211385595|gb|FL201907.1|FL201907
EST:     AAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACT                         GTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
genomic: AAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgata ... atatggatagGTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
EST: gi|211388218|gb|FL201911.1|FL201911
EST:     TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACT                         GTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
genomic: TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgata ... atatggatagGTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
EST: gi|60394760|gb|DN227630.1|DN227630
EST:     TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACT                         GTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA
genomic: TGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgata ... atatggatagGTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 106

TGATGCTCTATTAGCAGCTGAATCACGGGCTGAGAAAGCAAAGAAAGGAGTGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgata ... atatggatagGTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGAAGGCATTCTGCCGTTGTTGAATATGTTTTTAGTGGCCATCGGTTCAAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 151

TGATGCTCTATTAGCAGCTGAATCACGGGCTGAGAAAGCAAAGAAAGGAGTGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgata ... atatggatagGTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGAAGGCATTCTGCCGTTGTTGAATATGTTTTTAGTGGCCATCGGTTCAAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 129

TGATGCTCTATTAGCAGCTGAATCACGGGCTGAGAAAGCAAAGAAAGGAGTGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgata ... atatggatagGTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGAAGGCATTCTGCCGTTGTTGAATATGTTTTTAGTGGCCATCGGTTCAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 242

TGATGCTCTATTAGCAGCTGAATCACGGGCTGAGAAAGCAAAGAAAGGAGTGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgata ... atatggatagGTATCTGCAAAGAAGGCCAAAGATTTCCTTCCCTTCTTGCAGAGGAACAGAAGGCATTCTGCCGTTGTTGAATATGTTTTTAGTGGCCATCGGTTCAAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGCTCTATTAGCAGCTGAATCACGGGCTGAGAAAGCAAAGAAAGGAGTGCATTCTCAAAAAGAATCTCCTGTGATGCATATAACAGATTTAACAACTgtacgtgatattcatttattccatcagttcgattttgatattctctgcgtcatcattaacctatcagtgtggtccttatatggatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA