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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttcctcaatacatgaagcggtatcagtggaaatgtggatgcacatttgattgctgtgccatcttactatatattttcttaaatccagAAAAAGAGCGCATGATGAGCTGACTGCTGTGAATATTTTACCTTCTGCGTCTGGGACACAACAACAACATCGTCGACAATCAAGATTATGCCTTGTTTTG

Basic information

species Zea mays
transcript GRMZM2G070605_T01
intron # 11
splice site 3'
intron type U2

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|213168524|gb|FM182487.1|FM182487
EST:     GTGTTGCTATGTACTCTTACATTAAGGCTAAGATTGAAGAGGAGAAAAGG                         AAAAAGAGCGCATGATGAGCTGACTGCTGTGAATATTTTACCTTCTGCGTC
genomic: GTGTTGCTATGTACTCTTACATTAAGGCTAAGATTGAAGAGGAGAAAAGGgtgagttttc ... ttaaatccagAAAAAGAGCGCATGATGAGCTGACTGCTGTGAATATTTTACCTTCTGCGTC
EST: gi|32851134|gb|CD990815.1|CD990815
EST:     GTGTTGCTATGTACTCTTACATTAAGGCTAAGATTGAAGAGGAGAAAAGG                         AAAAAGAGCGCATGATGAGCTGACTGCTGTGAATATTTTACCTTCTGCGTC
genomic: GTGTTGCTATGTACTCTTACATTAAGGCTAAGATTGAAGAGGAGAAAAGGgtgagttttc ... ttaaatccagAAAAAGAGCGCATGATGAGCTGACTGCTGTGAATATTTTACCTTCTGCGTC

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), 39 (downstream exon)
Score: 17

CAACAAAATTAGCACACAAACTGGAATTGGCACGTCCATTGCCATAGCTGGTGTTGCTATGTACTCTTACATTAAGGCTAAGATTGAAGAGGAGAAAAGGgtgagttttc ... ttaaatccagAAAAAGAGCGCATGATGAGCTGACTGCTGTGAATATTTTACCTTCTGCGTCTGGGACACAACAACAACATCGTCGACAATCAAGATTATGCCTTGTTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 386

CAACAAAATTAGCACACAAACTGGAATTGGCACGTCCATTGCCATAGCTGGTGTTGCTATGTACTCTTACATTAAGGCTAAGATTGAAGAGGAGAAAAGGgtgagttttc ... ttaaatccagAAAAAGAGCGCATGATGAGCTGACTGCTGTGAATATTTTACCTTCTGCGTCTGGGACACAACAACAACATCGTCGACAATCAAGATTATGCCTTGTTTTG


Block sizes: 49 (upstream exon), 11 (downstream exon)
Score: 2

CAACAAAATTAGCACACAAACTGGAATTGGCACGTCCATTGCCATAGCTGGTGTTGCTATGTACTCTTACATTAAGGCTAAGATTGAAGAGGAGAAAAGGgtgagttttc ... ttaaatccagAAAAAGAGCGCATGATGAGCTGACTGCTGTGAATATTTTACCTTCTGCGTCTGGGACACAACAACAACATCGTCGACAATCAAGATTATGCCTTGTTTTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 139

CAACAAAATTAGCACACAAACTGGAATTGGCACGTCCATTGCCATAGCTGGTGTTGCTATGTACTCTTACATTAAGGCTAAGATTGAAGAGGAGAAAAGGgtgagttttc ... ttaaatccagAAAAAGAGCGCATGATGAGCTGACTGCTGTGAATATTTTACCTTCTGCGTCTGGGACACAACAACAACATCGTCGACAATCAAGATTATGCCTTGTTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggatgcacatttgattgctgtgccatcttactatatattttcttaaatccagAAAAAGAGCGCATGATGAGCTGACTGCTGTGAATATTTTACCTTCTGCGTCTGGGACACAACAACAACATCGTCGACAATCAAGATTATGCCTTGTTTTG
                           atcttac  putative branch site (score: 139)
                                      tattttctt  putative PPT
                           atcttactatatattt  TA-rich tract