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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCTCTCAACTATGACAAAGCTTATGAACTGCCTCCAGGCATTCCATCACACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAAgtaagtgaccatacttctttctgtattttcaagttcaagtcttgatcataagaaactaaagtactaaacattcttattgtaattcatccttttaaacata...

Basic information

species Zea mays
transcript GRMZM2G020040_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020040_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g48110.1 (Oryza sativa), 5'ss of exon 5
TCTCTCTCAACTATGACAAAGCTTATGAACTGCCTCCAGGCATTCCATCACACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAAgtaagtgaccatacttc-------tttctgta---ttttcaagttcaagtcttgatcataagaaactaaagtactaaacattcttattgtaattcatccttttaaacata
| ||| ||| |||||| ||||||| |||||||||||||||  || |||||||||| ||||  |||||||| |||||||| ||||||||||| || ||||||||||    |||| | |        || ||||   ||||   ||    ||  || | |||| || || ||  |   |  |   |||||  || |  |  ||         
TTTCTATCAGCTATGAAAAAGCTTCTGAACTGCCTCCAGGTGTTACATCACACAAATTTGTGGAGTATTCTGTATCAGGCCTGACAGATGCAAGCGAAAAgtaagcatgcataatgcatatcatcttatgtactttttttgtgtcatggtactgcttataacaagctgaa-catagagtacctttatttcaactgctattt---------
















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|8551700|gb|BE128856.1|BE128856
EST:     CACAAGTTTGCAGAGTATTCCGTATCAGGATTGACAGATGCCAGTGAAAA                         GTATGCAAACCGTAATTTATCTGCACCCATCAAAGCAAATCTACATTTTTC
genomic: CACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAAgtaagtgacc ... tctcaaccagGTATGCAAACCGTAATTTATCTGCACCCATCAAAGCAAATCTACATTTTTC
EST: gi|78179804|gb|DV550177.1|DV550177
EST:     CACAAGTTTGCAGAGTATTCCGTATCAGGATTGACAGATGCCAGTGAAAA                         GTATGCAAACCGTAATTTATCTGCACCCATCAAAGCAAATCTACATTTTTC
genomic: CACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAAgtaagtgacc ... tctcaaccagGTATGCAAACCGTAATTTATCTGCACCCATCAAAGCAAATCTACATTTTTC
EST: gi|13382246|gb|BG458921.1|BG458921
EST:     CACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAA                         GTATGCAAACCGTAATT
genomic: CACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAAgtaagtgacc ... tctcaaccagGTATGCAAACCGTAATT
EST: gi|32868507|gb|CF008189.1|CF008189
EST:     CACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAA                         GTATGCAAACCGTAATTTATCTGCACCCATCAAAGCAAATCTACATTTTTC
genomic: CACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAAgtaagtgacc ... tctcaaccagGTATGCAAACCGTAATTTATCTGCACCCATCAAAGCAAATCTACATTTTTC
EST: gi|12047102|gb|BF729241.1|BF729241
EST:     CACAAGTTTGCAGAGTATTCCGTATCAGGATTGACAGATGCCAGTGAAAA                         GTATGCAAACCGTAATTTATCTGCACCCATCAAAGCAAATCTACAT
genomic: CACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAAgtaagtgacc ... tctcaaccagGTATGCAAACCGTAATTTATCTGCACCCATCAAAGCAAATCTACAT

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), 45 (downstream exon)
Score: 84

TCTCTCTCAACTATGACAAAGCTTATGAACTGCCTCCAGGCATTCCATCACACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAAgtaagtgacc ... tctcaaccagGTATGCAAACCGTAATTTATCTGCACCCATCAAAGCAAATCTACATTTTTCTTTGAGTAGAAGTGGAATTATTGCTCTTGATAGAGCAGAAGCAGTAATT


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 101

TCTCTCTCAACTATGACAAAGCTTATGAACTGCCTCCAGGCATTCCATCACACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAAgtaagtgacc ... tctcaaccagGTATGCAAACCGTAATTTATCTGCACCCATCAAAGCAAATCTACATTTTTCTTTGAGTAGAAGTGGAATTATTGCTCTTGATAGAGCAGAAGCAGTAATT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 90

TCTCTCTCAACTATGACAAAGCTTATGAACTGCCTCCAGGCATTCCATCACACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAAgtaagtgacc ... tctcaaccagGTATGCAAACCGTAATTTATCTGCACCCATCAAAGCAAATCTACATTTTTCTTTGAGTAGAAGTGGAATTATTGCTCTTGATAGAGCAGAAGCAGTAATT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 248

TCTCTCTCAACTATGACAAAGCTTATGAACTGCCTCCAGGCATTCCATCACACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAAgtaagtgacc ... tctcaaccagGTATGCAAACCGTAATTTATCTGCACCCATCAAAGCAAATCTACATTTTTCTTTGAGTAGAAGTGGAATTATTGCTCTTGATAGAGCAGAAGCAGTAATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCTCTCAACTATGACAAAGCTTATGAACTGCCTCCAGGCATTCCATCACACAAGTTTGCAGAGTATTCCGTATCAGGACTGACAGATGCCAGTGAAAAgtaagtgaccatacttctttctgtattttcaagttcaagtcttgatcataagaaactaaagtactaaacattcttattgtaattcatccttttaaacata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataagaaa