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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacaaattatttctgaaagtttgcaggtcatgagcaatgtcgcaagtatctatataacatgctaattttatttaacagCAATGCTTATGGCAACAAGTTAAATGGAACCATTCCTCGTTCGCTGCGGAAACTTGAAAGCATGACCTATTT

Basic information

species Zea mays
transcript GRMZM5G809695_T03
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G809695_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 3'ss of exon 15
gtaagcacaaattatttctgaaagtttgcaggtcatgagcaatgtcgcaagtatctatataacatgctaattttatttaacagCAATGCTTATGGCAACAAGTTAAATGGAACCATTCCTCGTTCGCTGCGGAAACTTGAAAGCATGACCTATTT
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gtaagcatgatttaattataattgttatggtggaacttacaatttcagatgcatgtatctaatgtg--gattttcttta-cagCAATGCTTATGGCAACAGATTAAATGGGACCATTCCTCCTTCATTGCATAAACTTGAGAGCATGACTTATTT
















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|211377235|gb|FL413744.1|FL413744
EST:     GAAGGACCAATTCCTGACAACCTAAGTTCATGTGNGAATCTCAATAGCTT                         CAATGCTTATGGCAACAAG
genomic: GAAGGACCAATTCCTGACAACCTAAGTTCATGTGTGAATCTCAATAGCTTgtaagcacaa ... tatttaacagCAATGCTTATGGCAACAAG
EST: gi|31405872|gb|CD484604.1|CD484604
EST:     GAAGGACCAATTCCTGACAACCTAAGTTCATGTGTGAATCTCAATAGCTT                         CAATGCTTATGGCAACAAGTTAAATGGAACCATTCCTCGTTCGCTGCGGAA
genomic: GAAGGACCAATTCCTGACAACCTAAGTTCATGTGTGAATCTCAATAGCTTgtaagcacaa ... tatttaacagCAATGCTTATGGCAACAAGTTAAATGGAACCATTCCTCGTTCGCTGCGGAA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1225

GAACCTTGCGAATAACCACCTTGAAGGACCAATTCCTGACAACCTAAGTTCATGTGTGAATCTCAATAGCTTgtaagcacaa ... tatttaacagCAATGCTTATGGCAACAAGTTAAATGGAACCATTCCTCGTTCGCTGCGGAAACTTGAAAGCATGACCTATTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 55

GAACCTTGCGAATAACCACCTTGAAGGACCAATTCCTGACAACCTAAGTTCATGTGTGAATCTCAATAGCTTgtaagcacaa ... tatttaacagCAATGCTTATGGCAACAAGTTAAATGGAACCATTCCTCGTTCGCTGCGGAAACTTGAAAGCATGACCTATTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 93

GAACCTTGCGAATAACCACCTTGAAGGACCAATTCCTGACAACCTAAGTTCATGTGTGAATCTCAATAGCTTgtaagcacaa ... tatttaacagCAATGCTTATGGCAACAAGTTAAATGGAACCATTCCTCGTTCGCTGCGGAAACTTGAAAGCATGACCTATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggtcatgagcaatgtcgcaagtatctatataacatgctaattttatttaacagCAATGCTTATGGCAACAAGTTAAATGGAACCATTCCTCGTTCGCTGCGGAAACTTGAAAGCATGACCTATTT
                                    tgctaat  putative branch site (score: 93)
                                          ttttattt  CT-rich tract
                       tatctatataacatgc  TA-rich tract