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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgtacttctataccttatctgtctatgggtttatttcaaatttggcatgagttagccttctatgtggtattacctattggcgttttgctggactatcttttctcgtaatttattttaagtatttttagtcatgaagtgttttccttttaatttatttaaaacattttcaaacatcagGTTCAAGACAACAGTGAATATATGCATTCTGGACCGCCGTTTCTCATATTTCTTCATCCTGCTTTAGGCCCATTTTGGGATATCATACGACAAAAG

Basic information

species Zea mays
transcript AC197705.4_FGT011
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC197705.4_FGT011 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os05g39230.1 (Oryza sativa), 3'ss of exon 11
gtaattgtacttctataccttatctgtctatgggtttatttcaaatttggcatgagttagccttctatgtggtattacctattggcgttttgctggactatcttttctcgtaatttattttaagtatttttagtcatgaagtgttttccttttaatttatttaaaac----attttcaaacatcagGTTCAAGACAACAGTGAATATATGCATTCTGGACCGCCGTTTCTCATATTTCTTCATCCTGCTTTAGGCCCATTTTGGGATATCATACGACAAAAG
                                                                                      || | |    |  |     | | || |    |    | |  | ||   | ||   |   || ||  |   |||||||||       ||| | |   ||||||  |||||||| |||||||  ||| ||||||||| || ||||| ||||||||||||||||||||||| |||||||||||||||| | | || |||
-------------------------------------------------------------------------------------tgtctggtcaaaagacaaact-tagtgagcactgaccacttatattgtgcgtgggctacctttctaatggcttatttaaatttattctttcctattttcagGTCAAAGACAACTGTGAATACTTGCGTTCTGGACCACCTTTTCTTATATTTCTTCATCCTGCTTTAGGTCCATTTTGGGATATCACAAGGCAGAAG
















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: 45 (upstream exon), 45 (downstream exon)
Score: 20

ACTCCGGAGGGTTCACTCCTTGATATTATGCGTAATGCTCATGACCTCCTTTCCAGTTGCGGCATAGATATTCCCATGgtaattgtac ... caaacatcagGTTCAAGACAACAGTGAATATATGCATTCTGGACCGCCGTTTCTCATATTTCTTCATCCTGCTTTAGGCCCATTTTGGGATATCATACGACAAAAG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 35

ACTCCGGAGGGTTCACTCCTTGATATTATGCGTAATGCTCATGACCTCCTTTCCAGTTGCGGCATAGATATTCCCATGgtaattgtac ... caaacatcagGTTCAAGACAACAGTGAATATATGCATTCTGGACCGCCGTTTCTCATATTTCTTCATCCTGCTTTAGGCCCATTTTGGGATATCATACGACAAAAG


Block sizes: 41 (upstream exon), 45 (downstream exon)
Score: 13

ACTCCGGAGGGTTCACTCCTTGATATTATGCGTAATGCTCATGACCTCCTTTCCAGTTGCGGCATAGATATTCCCATGgtaattgtac ... caaacatcagGTTCAAGACAACAGTGAATATATGCATTCTGGACCGCCGTTTCTCATATTTCTTCATCCTGCTTTAGGCCCATTTTGGGATATCATACGACAAAAG


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 30

ACTCCGGAGGGTTCACTCCTTGATATTATGCGTAATGCTCATGACCTCCTTTCCAGTTGCGGCATAGATATTCCCATGgtaattgtac ... caaacatcagGTTCAAGACAACAGTGAATATATGCATTCTGGACCGCCGTTTCTCATATTTCTTCATCCTGCTTTAGGCCCATTTTGGGATATCATACGACAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagtcatgaagtgttttccttttaatttatttaaaacattttcaaacatcagGTTCAAGACAACAGTGAATATATGCATTCTGGACCGCCGTTTCTCATATTTCTTCATCCTGCTTTAGGCCCATTTTGGGATATCATACGACAAAAG
                      ttttaat  putative branch site (score: 30)
                                       cattttc  putative PPT
                ttttccttttaattta  TA-rich tract