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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtcatttcttctttccagcatttgactgagtagattgactataggtattgcttacttctggttgttttgttttgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATATTACACTTCTGTTCAACCTAGCATAAG

Basic information

species Zea mays
transcript GRMZM2G052926_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052926_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g36120.1 (Oryza sativa), 3'ss of exon 3
-----------gtgggtcatttcttctttccagcatttgactg---agtagattgactataggtattgcttacttctggttgttttgttttgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATATTACACTTCTGTTCAACCTAGCATAAG
            |  || ||||   ||     || | |  |||    ||||||      |   |  || ||| || |||  ||  | | | |||| |||||| ||||| || ||| ||||| | |||  ||| ||||| ||||||||||| |||| | |||||||||||||| ||||
gcgagttccttatccgttattttgcctgctatgcctgtagctgctaggtagatgtgtgctgatttatgtttattt-tgggggtggtttctggtggttcagGCACTTCTCCAAATGCAAGACTTGCATAATTCAGTGAGTGCGCTGCAATACTACAGTACTGTTCAACCTAGCGTAAG
















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|93284255|gb|EB676519.1|EB676519
EST:     AGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAA                         GCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATAT
genomic: AGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAAgtgggtcatt ... tgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATAT
EST: gi|31358368|gb|CD442725.1|CD442725
EST:     GTGCCAAGAACCAA                         GCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATAT
genomic: GTGCCAAGAACCAAgtgggtcatt ... tgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATAT
EST: gi|76013333|gb|DT940503.1|DT940503
EST:     AGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAA                         GCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATAT
genomic: AGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAAgtgggtcatt ... tgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATAT
EST: gi|78087001|gb|DV515394.1|DV515394
EST:     AGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAA                         GCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATAT
genomic: AGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAAgtgggtcatt ... tgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATAT
EST: gi|31250253|gb|CD219277.1|CD219277
EST:     AGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAA                         GCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATAT
genomic: AGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAAgtgggtcatt ... tgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATAT
EST: gi|78080905|gb|DV509317.1|DV509317
EST:     AGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAA                         GCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATAT
genomic: AGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAAgtgggtcatt ... tgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATAT

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: 436

TCTGATCTCCTTCAGCTGCTGCAGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAAgtgggtcatt ... tgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATATTACACTTCTGTTCAACCTAGCATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 295

TCTGATCTCCTTCAGCTGCTGCAGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAAgtgggtcatt ... tgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATATTACACTTCTGTTCAACCTAGCATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

TCTGATCTCCTTCAGCTGCTGCAGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAAgtgggtcatt ... tgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATATTACACTTCTGTTCAACCTAGCATAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 208

TCTGATCTCCTTCAGCTGCTGCAGCCGTTCGGCATGGTCTCCAAGATCGTCATGTTGCGTGCCAAGAACCAAgtgggtcatt ... tgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATATTACACTTCTGTTCAACCTAGCATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtagattgactataggtattgcttacttctggttgttttgttttgtggctcagGCTCTTCTGCAGATGGAAGACCTCCATGCTTCCGTGAGCGCGCTGCAATATTACACTTCTGTTCAACCTAGCATAAG
                     tgcttac  putative branch site (score: 208)
                                     ttttgtttt  putative PPT
                                     ttttgtttt  TA-rich tract