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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttggatctcgtggccgtgcttcatgcatctattagcgagttctggaagcttgggactgagcctgatcttgaccttgaaatttcctggttcgttctgctgtgctgcagGTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTGGATCAGGGAGGGGCCGTGTTGATGAGATTTACCTCAAACTGCGGACCAG

Basic information

species Zea mays
transcript GRMZM2G157462_T01
intron # 3
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|149108497|gb|EE292808.2|EE292808
EST:     CAAGTCCATCGTGCTGCAGATCGACAGCAAGTCGCAGCAGGTTTCCGCAA                         GTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTG
genomic: CAAGTCCATCGTGCTGCAGATCGACAGCAAGTCGCAGCAGGTTTCCGCAAgtaagttgga ... tgtgctgcagGTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTG
EST: gi|211132360|gb|FK982427.1|FK982427
EST:     CAAGTCCATCGTGCTGCAGATCGACAGCAAGTCGCAGCAGGTTTCCGCAA                         GTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTG
genomic: CAAGTCCATCGTGCTGCAGATCGACAGCAAGTCGCAGCAGGTTTCCGCAAgtaagttgga ... tgtgctgcagGTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTG
EST: gi|71773971|gb|DR971859.1|DR971859
EST:     CAAGTCCATCGTGCTGCAGATCGACAGCAAGTCGCAGCAGGTTTCCGCAA                         GTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTG
genomic: CAAGTCCATCGTGCTGCAGATCGACAGCAAGTCGCAGCAGGTTTCCGCAAgtaagttgga ... tgtgctgcagGTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTG
EST: gi|148945776|gb|EC891060.2|EC891060
EST:     CAAGTCCATCGTGCTGCAGATCGACAGCAAGTCGCAGCAGGTTTCCGCAA                         GTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTG
genomic: CAAGTCCATCGTGCTGCAGATCGACAGCAAGTCGCAGCAGGTTTCCGCAAgtaagttgga ... tgtgctgcagGTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTG

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: 104

ACGCGGGCGCCGATAGTGGTTGACCTGCAGAGGGAGCCGGGGCTCAGCAGCAAGTCCATCGTGCTGCAGATCGACAGCAAGTCGCAGCAGGTTTCCGCAAgtaagttgga ... tgtgctgcagGTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTGGATCAGGGAGGGGCCGTGTTGATGAGATTTACCTCAAACTGCGGACCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 101

ACGCGGGCGCCGATAGTGGTTGACCTGCAGAGGGAGCCGGGGCTCAGCAGCAAGTCCATCGTGCTGCAGATCGACAGCAAGTCGCAGCAGGTTTCCGCAAgtaagttgga ... tgtgctgcagGTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTGGATCAGGGAGGGGCCGTGTTGATGAGATTTACCTCAAACTGCGGACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

ACGCGGGCGCCGATAGTGGTTGACCTGCAGAGGGAGCCGGGGCTCAGCAGCAAGTCCATCGTGCTGCAGATCGACAGCAAGTCGCAGCAGGTTTCCGCAAgtaagttgga ... tgtgctgcagGTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTGGATCAGGGAGGGGCCGTGTTGATGAGATTTACCTCAAACTGCGGACCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 70

ACGCGGGCGCCGATAGTGGTTGACCTGCAGAGGGAGCCGGGGCTCAGCAGCAAGTCCATCGTGCTGCAGATCGACAGCAAGTCGCAGCAGGTTTCCGCAAgtaagttgga ... tgtgctgcagGTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTGGATCAGGGAGGGGCCGTGTTGATGAGATTTACCTCAAACTGCGGACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggactgagcctgatcttgaccttgaaatttcctggttcgttctgctgtgctgcagGTGCTCTCCGGCATTCACTGCAGGACAGACTCAGCAGGGGAGCATCTGGTGGATCAGGGAGGGGCCGTGTTGATGAGATTTACCTCAAACTGCGGACCAG
             tcttgac  putative branch site (score: 70)
                                       ttctgct  putative PPT
                     ttgaaattt  TA-rich tract