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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggaccagaatactaatccttttcatttattaaaattgctacctgcatacttatgttgtgtccttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG

Basic information

species Zea mays
transcript GRMZM2G082664_T01
intron # 4
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|211015453|gb|FL446495.1|FL446495
EST:     GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAG                         ATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
genomic: GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
EST: gi|71433814|gb|DR814864.1|DR814864
EST:     GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAG                         ATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
genomic: GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
EST: gi|76924992|gb|DV170232.1|DV170232
EST:     GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAG                         ATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
genomic: GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
EST: gi|148945041|gb|EC890225.2|EC890225
EST:     GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAG                         ATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
genomic: GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
EST: gi|149003162|gb|EE038900.2|EE038900
EST:     GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAG                         ATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
genomic: GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
EST: gi|211035971|gb|FL104471.1|FL104471
EST:     GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAG                         ATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
genomic: GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
EST: gi|211038407|gb|FL104474.1|FL104474
EST:     GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAG                         ATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
genomic: GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
EST: gi|149028361|gb|EE286119.2|EE286119
EST:     GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAG                         ATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
genomic: GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
EST: gi|88758154|gb|DY542295.1|DY542295
EST:     GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAG                         ATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
genomic: GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
EST: gi|211038406|gb|FL104473.1|FL104473
EST:     GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAG                         ATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
genomic: GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
EST: gi|116827363|gb|EC871258.1|EC871258
EST:     GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAG                         ATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
genomic: GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
EST: gi|211038408|gb|FL104475.1|FL104475
EST:     GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAG                         ATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
genomic: GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG

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: 37 (upstream exon), 34 (downstream exon)
Score: 155

GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG


Block sizes: 37 (upstream exon), 34 (downstream exon)
Score: 213

GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG


Block sizes: 37 (upstream exon), 41 (downstream exon)
Score: 121

GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG


Block sizes: 37 (upstream exon), 34 (downstream exon)
Score: 398

GCCATCAATTCTAGCATCTCTGGGCGCACATTACAAGgtgggaccag ... cttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttcatttattaaaattgctacctgcatacttatgttgtgtccttattgcagATCCCCATGCCAGCCCGCTGGTTCTCATCTACAG
                                           tccttatt  CT-rich tract
       atttattaaaattgct  TA-rich tract