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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttttgttctatcattttttgtgtgaatatcaaataaggtgcgagaaaactacttgcttatgttagttccattaatatacaaaattttgattgcagtcactctgacaagaatgtatctgtctttctctgggtaattgatttcttgtgcaaattctgtagCTATGTGTGTGGAGTATTGATGGCTGGGAAAAAAAGAAATCAAGATATATCCAACCCCCAGCAAACCGACCTGGCACTTTGGTTGGTGACACAAGGGTGC

Basic information

species Zea mays
transcript GRMZM2G042992_T01
intron # 22
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|60357392|gb|DN224365.1|DN224365
EST:     CCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAG                         CTATGTGTGTGGAGTATTGATGGCTGGGNNNNNNNGAAATCAAGATATATC
genomic: CCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAGgtaggttttg ... aattctgtagCTATGTGTGTGGAGTATTGATGGCTGGGAAAAAAAGAAATCAAGATATATC
EST: gi|76934579|gb|DV173944.1|DV173944
EST:     CCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAG                         CTATGTGTGTGGAGTATTGATGGCTGGGNNNNNNNGAAATCAAGATATATC
genomic: CCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAGgtaggttttg ... aattctgtagCTATGTGTGTGGAGTATTGATGGCTGGGAAAAAAAGAAATCAAGATATATC
EST: gi|89761150|gb|DY689280.1|DY689280
EST:     CCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAG                         CTATGTGTGTGGAGTATTGATGGCTGGGNNNNNNNGAAATCAAGATATATC
genomic: CCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAGgtaggttttg ... aattctgtagCTATGTGTGTGGAGTATTGATGGCTGGGAAAAAAAGAAATCAAGATATATC
EST: gi|89764406|gb|DY691228.1|DY691228
EST:     CCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAG                         CTATGTGTGTGGAGTATTGATGGCTGGGNNNNNNNGAAATCAAGATATATC
genomic: CCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAGgtaggttttg ... aattctgtagCTATGTGTGTGGAGTATTGATGGCTGGGAAAAAAAGAAATCAAGATATATC
EST: gi|60349882|gb|DN216855.1|DN216855
EST:     CCTTTTCTC-ATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAG                         CTATGTGTGTGGAGTATTGATGGCTGGGNNNNNNNGAAATCAAGATATATC
genomic: CCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAGgtaggttttg ... aattctgtagCTATGTGTGTGGAGTATTGATGGCTGGGAAAAAAAGAAATCAAGATATATC
EST: gi|89764424|gb|DY691240.1|DY691240
EST:     CCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAG                         CTATGTGTGTGGAGTATTGATGGCTGGGNNNNNNNGAAATCAAGATATATC
genomic: CCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAGgtaggttttg ... aattctgtagCTATGTGTGTGGAGTATTGATGGCTGGGAAAAAAAGAAATCAAGATATATC

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), 47 (downstream exon)
Score: 753

GTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAGgtaggttttg ... aattctgtagCTATGTGTGTGGAGTATTGATGGCTGGGAAAAAAAGAAATCAAGATATATCCAACCCCCAGCAAACCGACCTGGCACTTTGGTTGGTGACACAAGGGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

GTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAGgtaggttttg ... aattctgtagCTATGTGTGTGGAGTATTGATGGCTGGGAAAAAAAGAAATCAAGATATATCCAACCCCCAGCAAACCGACCTGGCACTTTGGTTGGTGACACAAGGGTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 294

GTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAGgtaggttttg ... aattctgtagCTATGTGTGTGGAGTATTGATGGCTGGGAAAAAAAGAAATCAAGATATATCCAACCCCCAGCAAACCGACCTGGCACTTTGGTTGGTGACACAAGGGTGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 311

GTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAGgtaggttttg ... aattctgtagCTATGTGTGTGGAGTATTGATGGCTGGGAAAAAAAGAAATCAAGATATATCCAACCCCCAGCAAACCGACCTGGCACTTTGGTTGGTGACACAAGGGTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaagaatgtatctgtctttctctgggtaattgatttcttgtgcaaattctgtagCTATGTGTGTGGAGTATTGATGGCTGGGAAAAAAAGAAATCAAGATATATCCAACCCCCAGCAAACCGACCTGGCACTTTGGTTGGTGACACAAGGGTGC
                           taattgattt  TA-rich tract