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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccctaaatatgttgactgaaatatattataaatggatttgaggagggtatcaaatttgtaaaactgaactttctttgttctgattccccctcccattagGATCAATTGAGGGTCGAATGCTTCAATGGTTCCAGAAAGCTTCAAGCACAATAGTGTCAAATGTTTCCATTGATGCCATAAAGCATATTCAAGATTTTGA

Basic information

species Zea mays
transcript GRMZM2G524711_T02
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|211472158|gb|FK973007.1|FK973007
EST:     GATGTTGGCATCAATTGGTAAGGGTCACTATGCTGCTGCATTTGATACAG                         GATCAATTGAGGGTCGAATGCTTCAATGGTTCCAGAAAGCTTCAAGCACAA
genomic: GATGTTGGCATCAATTGGTAAGGGTCACTATGCTGCTGCATTTGATACAGgtatgggcat ... ctcccattagGATCAATTGAGGGTCGAATGCTTCAATGGTTCCAGAAAGCTTCAAGCACAA
EST: gi|148932235|gb|EC875748.2|EC875748
EST:     GATGTTGGCATCAATTGGTAAGGGTCACTATGCTGCTGCATTTGATACAG                         GATCAATTGAGGGTCGAATGCTTCAATGGTTCCAGAAAGCTTCAAGCACAA
genomic: GATGTTGGCATCAATTGGTAAGGGTCACTATGCTGCTGCATTTGATACAGgtatgggcat ... ctcccattagGATCAATTGAGGGTCGAATGCTTCAATGGTTCCAGAAAGCTTCAAGCACAA

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: 111

GTTCATATTGCAACCACTATTTCTTGAGGATGTTGGCATCAATTGGTAAGGGTCACTATGCTGCTGCATTTGATACAGgtatgggcat ... ctcccattagGATCAATTGAGGGTCGAATGCTTCAATGGTTCCAGAAAGCTTCAAGCACAATAGTGTCAAATGTTTCCATTGATGCCATAAAGCATATTCAAGATTTTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

GTTCATATTGCAACCACTATTTCTTGAGGATGTTGGCATCAATTGGTAAGGGTCACTATGCTGCTGCATTTGATACAGgtatgggcat ... ctcccattagGATCAATTGAGGGTCGAATGCTTCAATGGTTCCAGAAAGCTTCAAGCACAATAGTGTCAAATGTTTCCATTGATGCCATAAAGCATATTCAAGATTTTGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 81

GTTCATATTGCAACCACTATTTCTTGAGGATGTTGGCATCAATTGGTAAGGGTCACTATGCTGCTGCATTTGATACAGgtatgggcat ... ctcccattagGATCAATTGAGGGTCGAATGCTTCAATGGTTCCAGAAAGCTTCAAGCACAATAGTGTCAAATGTTTCCATTGATGCCATAAAGCATATTCAAGATTTTGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 124

GTTCATATTGCAACCACTATTTCTTGAGGATGTTGGCATCAATTGGTAAGGGTCACTATGCTGCTGCATTTGATACAGgtatgggcat ... ctcccattagGATCAATTGAGGGTCGAATGCTTCAATGGTTCCAGAAAGCTTCAAGCACAATAGTGTCAAATGTTTCCATTGATGCCATAAAGCATATTCAAGATTTTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtatcaaatttgtaaaactgaactttctttgttctgattccccctcccattagGATCAATTGAGGGTCGAATGCTTCAATGGTTCCAGAAAGCTTCAAGCACAATAGTGTCAAATGTTTCCATTGATGCCATAAAGCATATTCAAGATTTTGA
                                 ttctgat  putative branch site (score: 124)
                        ctttctttgttctgat  CT-rich tract
     tcaaatttgtaaaa  TA-rich tract