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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttttttactgagattcacatttcttttacttactgttctcattgaaacatatttgcatttctacagGACAAAGATTCAATGCCATCTTCAAGTCGTGATAACCTAAAAAGCTTTG

Basic information

species Zea mays
transcript GRMZM2G421899_T02
intron # 5
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|78076015|gb|DV504449.1|DV504449
EST:     ATGCTCACCGCCTCCTTGCCAATGGCACTTATGGGGATAACATTTTGAAG                         GACAAAGATTCAATGCCATCTTCAAGTCGTGATAACCTAAAAAGCTTTG
genomic: ATGCTCACCGCCTCCTTGCCAATGGCACTTATGGGGATAACATTTTGAAGgtaatttttt ... atttctacagGACAAAGATTCAATGCCATCTTCAAGTCGTGATAACCTAAAAAGCTTTG




















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: 18

TTCTGCCAGAGTTAGAAGGGATGTTGCAGCACGTGCTATGCAGGGTTGGCATGCTCACCGCCTCCTTGCCAATGGCACTTATGGGGATAACATTTTGAAGgtaatttttt ... atttctacagGACAAAGATTCAATGCCATCTTCAAGTCGTGATAACCTAAAAAGCTTTG


Block sizes: 44 (upstream exon), 14 (downstream exon)
Score: 5

TTCTGCCAGAGTTAGAAGGGATGTTGCAGCACGTGCTATGCAGGGTTGGCATGCTCACCGCCTCCTTGCCAATGGCACTTATGGGGATAACATTTTGAAGgtaatttttt ... atttctacagGACAAAGATTCAATGCCATCTTCAAGTCGTGATAACCTAAAAAGCTTTG


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 6

TTCTGCCAGAGTTAGAAGGGATGTTGCAGCACGTGCTATGCAGGGTTGGCATGCTCACCGCCTCCTTGCCAATGGCACTTATGGGGATAACATTTTGAAGgtaatttttt ... atttctacagGACAAAGATTCAATGCCATCTTCAAGTCGTGATAACCTAAAAAGCTTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 20

TTCTGCCAGAGTTAGAAGGGATGTTGCAGCACGTGCTATGCAGGGTTGGCATGCTCACCGCCTCCTTGCCAATGGCACTTATGGGGATAACATTTTGAAGgtaatttttt ... atttctacagGACAAAGATTCAATGCCATCTTCAAGTCGTGATAACCTAAAAAGCTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattcacatttcttttacttactgttctcattgaaacatatttgcatttctacagGACAAAGATTCAATGCCATCTTCAAGTCGTGATAACCTAAAAAGCTTTG
               tacttac  putative branch site (score: 20)
                                            catttct  putative PPT
       atttcttttactta  TA-rich tract