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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctttccttttcatgaagtgcttagtcatttacattaataactatagaagaaatcaagtctgacggtatgttattcccaataattgttagGGGTGGAGAAAAAAGAAGCCAACAGGGAGGTTCCAGCTCTCAAAATGATTCATCACATTTCCCCCCTGAGTGATAGTTCAGTTAGCGTCGTACGGATGTA

Basic information

species Zea mays
transcript GRMZM5G871262_T02
intron # 13
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|78121981|gb|DV540365.1|DV540365
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTATTATGCTATATTT                         GGGTGGAGAAAAAAGAAGCCAACAGGGAGGTTCCAGCTCTCAAAATGATTC
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTTgtaagtcctt ... taattgttagGGGTGGAGAAAAAAGAAGCCAACAGGGAGGTTCCAGCTCTCAAAATGATTC
EST: gi|89251977|gb|DY623763.1|DY623763
EST:     ATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTT                         GGGTGGAGAAAAAAGAAGCCAACAGGGAGGTTCCAGCTCTCAAAATGATTC
genomic: ATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTTgtaagtcctt ... taattgttagGGGTGGAGAAAAAAGAAGCCAACAGGGAGGTTCCAGCTCTCAAAATGATTC

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: 153

GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTTgtaagtcctt ... taattgttagGGGTGGAGAAAAAAGAAGCCAACAGGGAGGTTCCAGCTCTCAAAATGATTCATCACATTTCCCCCCTGAGTGATAGTTCAGTTAGCGTCGTACGGATGTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 105

GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTTgtaagtcctt ... taattgttagGGGTGGAGAAAAAAGAAGCCAACAGGGAGGTTCCAGCTCTCAAAATGATTCATCACATTTCCCCCCTGAGTGATAGTTCAGTTAGCGTCGTACGGATGTA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 129

GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTTgtaagtcctt ... taattgttagGGGTGGAGAAAAAAGAAGCCAACAGGGAGGTTCCAGCTCTCAAAATGATTCATCACATTTCCCCCCTGAGTGATAGTTCAGTTAGCGTCGTACGGATGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTTgtaagtcctt ... taattgttagGGGTGGAGAAAAAAGAAGCCAACAGGGAGGTTCCAGCTCTCAAAATGATTCATCACATTTCCCCCCTGAGTGATAGTTCAGTTAGCGTCGTACGGATGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taataactatagaagaaatcaagtctgacggtatgttattcccaataattgttagGGGTGGAGAAAAAAGAAGCCAACAGGGAGGTTCCAGCTCTCAAAATGATTCATCACATTTCCCCCCTGAGTGATAGTTCAGTTAGCGTCGTACGGATGTA
                                           aataattgtta  TA-rich tract