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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTGCTAAGGAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAGgttagtcatctagtcctgttatttatttttcaagcatattgtagttgcacacttgatgtttgattgctttgttttcacttatag

Basic information

species Zea mays
transcript GRMZM2G126079_T01
intron # 4
splice site 5'
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|71298677|gb|DR785313.1|DR785313
EST:     GAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAG                         TGATGTACATAGACTCAGAAATTTCATCAAGAATGTATATGTTGAACGGAG
genomic: GAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAGgttagtcatc ... tcacttatagTGATGTACATAGACTCAGAAATTTCATCAAGAATGTATATGTTGAACGGAG
EST: gi|50323334|gb|CO518460.1|CO518460
EST:     GAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAG                         TGATGTACATAGACTCAGAAATTTCATCAAG
genomic: GAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAGgttagtcatc ... tcacttatagTGATGTACATAGACTCAGAAATTTCATCAAG
EST: gi|148951394|gb|EC897111.2|EC897111
EST:     GAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAG                         TGATGTACATAGACTCAGAAATTTCATCAAGAATGTATATGTTGAACGGAG
genomic: GAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAGgttagtcatc ... tcacttatagTGATGTACATAGACTCAGAAATTTCATCAAGAATGTATATGTTGAACGGAG
EST: gi|74243474|gb|DT651388.1|DT651388
EST:     GAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAG                         TGATGTACATAGACTCAGAAATTTCATCAAGAATGTATATGTTGAACGGAG
genomic: GAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAGgttagtcatc ... tcacttatagTGATGTACATAGACTCAGAAATTTCATCAAGAATGTATATGTTGAACGGAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 21

CGTGCTAAGGAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAGgttagtcatc ... tcacttatagTGATGTACATAGACTCAGAAATTTCATCAAGAATGTATATGTTGAACGGAGATATTCAGACCAAAGAATTGGCGAACATTTAGCGCAAGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

CGTGCTAAGGAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAGgttagtcatc ... tcacttatagTGATGTACATAGACTCAGAAATTTCATCAAGAATGTATATGTTGAACGGAGATATTCAGACCAAAGAATTGGCGAACATTTAGCGCAAGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

CGTGCTAAGGAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAGgttagtcatc ... tcacttatagTGATGTACATAGACTCAGAAATTTCATCAAGAATGTATATGTTGAACGGAGATATTCAGACCAAAGAATTGGCGAACATTTAGCGCAAGCAAAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 5

CGTGCTAAGGAAATCTATTTCAAGCATTGGGACTTGCAAGGCCCTGTTATTGACAGTAGgttagtcatc ... tcacttatagTGATGTACATAGACTCAGAAATTTCATCAAGAATGTATATGTTGAACGGAGATATTCAGACCAAAGAATTGGCGAACATTTAGCGCAAGCAAAG