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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaatggattctacttttttatgtggttctactcatcctttcttcatgaagactcggtgctcaattgacatgctatatttggactgtgtttcagTACCAAAATGACTACAAGGTGATAAACATGGATCAGTGGATGGGATTTATGCGGTTCTGTAATGAGGTCATGTTTTAAATATTACATATGTTGCAGCATT

Basic information

species Zea mays
transcript GRMZM2G067067_T01
intron # 8
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|211009144|gb|FL186797.1|FL186797
EST:     TAGGCTTGCAGTTCCGCCCTCAGGTTGACAAGCTTARTAATTACCTCAAG                         TACCAAAATGACTACAAGGKGATAAACATGGATCAGTGGATGGGATTTATG
genomic: TAGGCTTGCAGTTCCGCCCTCAGGTTGACAAGCTTAGTAATTACCTCAAGgcaatggatt ... tgtgtttcagTACCAAAATGACTACAAGGTGATAAACATGGATCAGTGGATGGGATTTATG
EST: gi|32864042|gb|CF003724.1|CF003724
EST:     TAGGCTTGCAGTTCCGCCCTCAGGTTGACAAGCTTAGTAATTACCTCAAG                         TACCAAAATGACTACAAGGTGATAAACATGGATCAGTGGATGGGATTTATG
genomic: TAGGCTTGCAGTTCCGCCCTCAGGTTGACAAGCTTAGTAATTACCTCAAGgcaatggatt ... tgtgtttcagTACCAAAATGACTACAAGGTGATAAACATGGATCAGTGGATGGGATTTATG
EST: gi|74233001|gb|DT640915.1|DT640915
EST:     TAGGCTTGCAGTTCCGCCCTCAGGTTGACAAGCTTAGTAATTACCTCAAG                         TACCAAAATGACTACAAGGTGATAAACATGGATCAGTGGATGGGATTTATG
genomic: TAGGCTTGCAGTTCCGCCCTCAGGTTGACAAGCTTAGTAATTACCTCAAGgcaatggatt ... tgtgtttcagTACCAAAATGACTACAAGGTGATAAACATGGATCAGTGGATGGGATTTATG

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: 46 (upstream exon), 49 (downstream exon)
Score: 99

GAAGAAGTGTATAGAAATACCAGTTGCTTGTGAGTTGCTGAATCTAGTATTAGGCTTGCAGTTCCGCCCTCAGGTTGACAAGCTTAGTAATTACCTCAAGgcaatggatt ... tgtgtttcagTACCAAAATGACTACAAGGTGATAAACATGGATCAGTGGATGGGATTTATGCGGTTCTGTAATGAGGTCATGTTTTAAATATTACATATGTTGCAGCATT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 79

GAAGAAGTGTATAGAAATACCAGTTGCTTGTGAGTTGCTGAATCTAGTATTAGGCTTGCAGTTCCGCCCTCAGGTTGACAAGCTTAGTAATTACCTCAAGgcaatggatt ... tgtgtttcagTACCAAAATGACTACAAGGTGATAAACATGGATCAGTGGATGGGATTTATGCGGTTCTGTAATGAGGTCATGTTTTAAATATTACATATGTTGCAGCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

GAAGAAGTGTATAGAAATACCAGTTGCTTGTGAGTTGCTGAATCTAGTATTAGGCTTGCAGTTCCGCCCTCAGGTTGACAAGCTTAGTAATTACCTCAAGgcaatggatt ... tgtgtttcagTACCAAAATGACTACAAGGTGATAAACATGGATCAGTGGATGGGATTTATGCGGTTCTGTAATGAGGTCATGTTTTAAATATTACATATGTTGCAGCATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

GAAGAAGTGTATAGAAATACCAGTTGCTTGTGAGTTGCTGAATCTAGTATTAGGCTTGCAGTTCCGCCCTCAGGTTGACAAGCTTAGTAATTACCTCAAGgcaatggatt ... tgtgtttcagTACCAAAATGACTACAAGGTGATAAACATGGATCAGTGGATGGGATTTATGCGGTTCTGTAATGAGGTCATGTTTTAAATATTACATATGTTGCAGCATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcatgaagactcggtgctcaattgacatgctatatttggactgtgtttcagTACCAAAATGACTACAAGGTGATAAACATGGATCAGTGGATGGGATTTATGCGGTTCTGTAATGAGGTCATGTTTTAAATATTACATATGTTGCAGCATT
                       aattgac  putative branch site (score: 103)
                                  tatattt  TA-rich tract