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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttcgccgccttcgccttacagttagaatctgtttttttgttgttgttgtccttttatctgtacacactgtcggagcattccgcttcatctgattcacatgaaaaccctacctctatctatctgtctgctagGACGTTTCTCCGCCAGAGCTCCTGCGCTTCATGCGGGAGCAGCGGTCGCAGTGGGCCGACAGCAATCTAGACGCGTTCTTCGCTTCTGCGATGAAACCGG

Basic information

species Zea mays
transcript AC187157.4_FGT005
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC187157.4_FGT005 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g10320.1 (Oryza sativa), 3'ss of exon 7
gtgagcttcgccgccttcgccttacagttagaatctgtttttttgttgttgttgtccttttatctgtacacactgtcggagcattccgcttcatctgattcacatgaaaaccctacctctatctatctgtctgctagGACGTTTCTCCGCCAGAGCTCCTGCGCTTCATGCGGGAGCAGCGGTCGCAGTGGGCCGACAGCAATCTAGACGCGTTCTTCGCTTCTGCGATGAAACCGG
         |    |||| |  |  |  ||||||   | ||||| |||||                       ||   || |||   |     | |  |||| |  |      ||  |||      |||| |||||||| || ||||| |||   || ||||  ||  |||| || || ||||| |||||||||||||||||| ||||||| |||||||| ||  ||||||||||  
---------gttagcttcactatgaaactagaattaatattttttttgtt-----------------------tggttgatcat---gtccagtttttttcatacaa------tatttctg-----ctgtttgctagGATGTCTCTCCTCCATCACTACTGCAATTTTTGCGCGAACACCGGTCACAGTGGGCCGACAGCAATTTAGACGCATTCTTCGCCTCCACGATGAAACCAA
















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|22543133|gb|BU093571.1|BU093571
EST:     ATCGATGCTGCTGCAG                         GATGTTTCTCCGCCAGAGCTCCTGCGCTTCATGCGCGAGCAGCGGTCGCAG
genomic: ATCGATGCTGCTGCAGgtgagcttcg ... tgtctgctagGACGTTTCTCCGCCAGAGCTCCTGCGCTTCATGCGGGAGCAGCGGTCGCAG
EST: gi|88758540|gb|DY542909.1|DY542909
EST:     GCACTGGCAGCAGCAGTGTGCTCTGCGCAAAGGCATCGATGCTGCTGCAG                         GATGTTTCTCCGCCAGAGCTCCTGCGCTTCATG
genomic: GCACTGGCAGCAGCAGTGTGCTCTGCGCAAAGGCATCGATGCTGCTGCAGgtgagcttcg ... tgtctgctagGACGTTTCTCCGCCAGAGCTCCTGCGCTTCATG
EST: gi|26457082|gb|CA828665.1|CA828665
EST:     GGCAGCAGCAGTGTGCTCTGCGCAAAGGCATCGATGCTGCTGCAG                         GATGTTTCTCCGCCAGAGCTCCTGCGCTTCATGCGCGAGCAGCGGTCGCAG
genomic: GGCAGCAGCAGTGTGCTCTGCGCAAAGGCATCGATGCTGCTGCAGgtgagcttcg ... tgtctgctagGACGTTTCTCCGCCAGAGCTCCTGCGCTTCATGCGGGAGCAGCGGTCGCAG

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: 42 (upstream exon), 47 (downstream exon)
Score: 21

GAGTAGAGTGGTCAGCTGCAATGCAACTTTCAGTAACGGACCTGTAGTCGGCACTGGCAGCAGCAGTGTGCTCTGCGCAAAGGCATCGATGCTGCTGCAGgtgagcttcg ... tgtctgctagGACGTTTCTCCGCCAGAGCTCCTGCGCTTCATGCGGGAGCAGCGGTCGCAGTGGGCCGACAGCAATCTAGACGCGTTCTTCGCTTCTGCGATGAAACCGG


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

GAGTAGAGTGGTCAGCTGCAATGCAACTTTCAGTAACGGACCTGTAGTCGGCACTGGCAGCAGCAGTGTGCTCTGCGCAAAGGCATCGATGCTGCTGCAGgtgagcttcg ... tgtctgctagGACGTTTCTCCGCCAGAGCTCCTGCGCTTCATGCGGGAGCAGCGGTCGCAGTGGGCCGACAGCAATCTAGACGCGTTCTTCGCTTCTGCGATGAAACCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

GAGTAGAGTGGTCAGCTGCAATGCAACTTTCAGTAACGGACCTGTAGTCGGCACTGGCAGCAGCAGTGTGCTCTGCGCAAAGGCATCGATGCTGCTGCAGgtgagcttcg ... tgtctgctagGACGTTTCTCCGCCAGAGCTCCTGCGCTTCATGCGGGAGCAGCGGTCGCAGTGGGCCGACAGCAATCTAGACGCGTTCTTCGCTTCTGCGATGAAACCGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 16

GAGTAGAGTGGTCAGCTGCAATGCAACTTTCAGTAACGGACCTGTAGTCGGCACTGGCAGCAGCAGTGTGCTCTGCGCAAAGGCATCGATGCTGCTGCAGgtgagcttcg ... tgtctgctagGACGTTTCTCCGCCAGAGCTCCTGCGCTTCATGCGGGAGCAGCGGTCGCAGTGGGCCGACAGCAATCTAGACGCGTTCTTCGCTTCTGCGATGAAACCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attccgcttcatctgattcacatgaaaaccctacctctatctatctgtctgctagGACGTTTCTCCGCCAGAGCTCCTGCGCTTCATGCGGGAGCAGCGGTCGCAGTGGGCCGACAGCAATCTAGACGCGTTCTTCGCTTCTGCGATGAAACCGG
          atctgat  putative branch site (score: 16)
                                       tctatct  putative PPT
                     atgaaaa  TA-rich tract