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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaactcttctatctatcattataatttcgcctcgaatccactagcttttgtttcttgaacagtccatgtctgatatctggtttttttctccttcatgtggctattggcaagATATTAATGAATGCATCACCAGAAATCCGTGCACCAATAGGTGCTCAAACACAATAGGTGGTTTCCAGTGCACGTGCCCAGCAGGGATGAGCGGCGACGG

Basic information

species Zea mays
transcript GRMZM2G176225_T01
intron # 1
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|13178161|gb|BG349419.1|BG349419
EST:     CAGTGGATTCGAGGGGAACCCATACCTGCAAGGGCCAAATGGATGCACAG                         ATATTAATGAATGCATCACCAGAAATCCGTGCACCAATAGGTGCTCAAACA
genomic: CAGTGGATTCGAGGGGAACCCATACCTGCAAGGGCCAAATGGATGCACAGgtaacaaact ... tattggcaagATATTAATGAATGCATCACCAGAAATCCGTGCACCAATAGGTGCTCAAACA
EST: gi|9731814|gb|BE510566.1|BE510566
EST:     CAGTGGATTCGAGGGGAACCCATACCTGCAAGGGCCAAATGGATGCACAG                         ATATTAATGAATGCATCACCAGAAATCCGTGCACCAATAGGTGCTCAAACA
genomic: CAGTGGATTCGAGGGGAACCCATACCTGCAAGGGCCAAATGGATGCACAGgtaacaaact ... tattggcaagATATTAATGAATGCATCACCAGAAATCCGTGCACCAATAGGTGCTCAAACA
EST: gi|13178481|gb|BG349739.1|BG349739
EST:     CAGTGGATTCGAGGGGAACCCATACCTGCAAGGGCCAAATGGATGCACAG                         ATATTAATGAATGCATCACCAGAAATCCGTGCACCAATAGGTGCTCAAACA
genomic: CAGTGGATTCGAGGGGAACCCATACCTGCAAGGGCCAAATGGATGCACAGgtaacaaact ... tattggcaagATATTAATGAATGCATCACCAGAAATCCGTGCACCAATAGGTGCTCAAACA

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 3 RNA-Seq libraries.


Block sizes: 43 (upstream exon), 20 (downstream exon)
Score: 6

GCCTACTGCTACAACTCATCAAACGGAATCGGTTACCGCTGCAATTGCTCCAGTGGATTCGAGGGGAACCCATACCTGCAAGGGCCAAATGGATGCACAGgtaacaaact ... tattggcaagATATTAATGAATGCATCACCAGAAATCCGTGCACCAATAGGTGCTCAAACACAATAGGTGGTTTCCAGTGCACGTGCCCAGCAGGGATGAGCGGCGACGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 36

GCCTACTGCTACAACTCATCAAACGGAATCGGTTACCGCTGCAATTGCTCCAGTGGATTCGAGGGGAACCCATACCTGCAAGGGCCAAATGGATGCACAGgtaacaaact ... tattggcaagATATTAATGAATGCATCACCAGAAATCCGTGCACCAATAGGTGCTCAAACACAATAGGTGGTTTCCAGTGCACGTGCCCAGCAGGGATGAGCGGCGACGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 14

GCCTACTGCTACAACTCATCAAACGGAATCGGTTACCGCTGCAATTGCTCCAGTGGATTCGAGGGGAACCCATACCTGCAAGGGCCAAATGGATGCACAGgtaacaaact ... tattggcaagATATTAATGAATGCATCACCAGAAATCCGTGCACCAATAGGTGCTCAAACACAATAGGTGGTTTCCAGTGCACGTGCCCAGCAGGGATGAGCGGCGACGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacagtccatgtctgatatctggtttttttctccttcatgtggctattggcaagATATTAATGAATGCATCACCAGAAATCCGTGCACCAATAGGTGCTCAAACACAATAGGTGGTTTCCAGTGCACGTGCCCAGCAGGGATGAGCGGCGACGG
           gtctgat  putative branch site (score: 14)
 tttttttct  TA-rich tract