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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcatggtgctgcttttatgatagattttttgcttgcaaatgttaagatggtctaaccaatttgtcacactgctctttcttaatattctgtgagctatgtttcacatgtgctttgaacttgttatataccaatgctgatgtaaaatttgagctaacatgtttttcgttcctaccttttgcactgtcagCATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAG

Basic information

species Zea mays
transcript GRMZM2G116086_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|22935976|gb|BU572251.1|BU572251
EST:     GCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAG                         CATCTAGATGGCAAGGAATCAGGGTCATCTGGACAACATGCTGAATATGAT
genomic: GCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAGgtacgtcatg ... gcactgtcagCATCTAGATGG-AAGGAATCAGGGTCATCTGGACAACATGTTGAATATGAT
EST: gi|67028330|gb|CO457079.1|CO457079
EST:     GCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAG                         CATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATC
genomic: GCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAGgtacgtcatg ... gcactgtcagCATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATC
EST: gi|6865205|gb|AW360555.1|AW360555
EST:     GACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAG                         CATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATC
genomic: GACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAGgtacgtcatg ... gcactgtcagCATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATC
EST: gi|87155883|gb|DY400672.1|DY400672
EST:     GCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAG                         CATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATC
genomic: GCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAGgtacgtcatg ... gcactgtcagCATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATC
EST: gi|26559656|gb|CA831891.1|CA831891
EST:     GCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAG                         CATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATC
genomic: GCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAGgtacgtcatg ... gcactgtcagCATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATC

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: 556

GTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAGgtacgtcatg ... gcactgtcagCATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 436

GTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAGgtacgtcatg ... gcactgtcagCATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 397

GTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAGgtacgtcatg ... gcactgtcagCATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 768

GTTTGTTCATGGAGACGTTAAACCCGAGAATTTTCTACTTGGCCAGCCTGGATCCCCTGACGAGAAAAAACTTTTTCTGATTGATCTTGGGTTAGgtacgtcatg ... gcactgtcagCATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgatgtaaaatttgagctaacatgtttttcgttcctaccttttgcactgtcagCATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAG
                agctaac  putative branch site (score: 768)
                          tttttcgttcctacct  putative PPT
     tgtaaaattt  TA-rich tract