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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgatgatgttctgcttcattccagattccacctatcagattttttttttcaagaagtttagattcattggttggtatggaatgaacattaggaatgatcggttattccttcttgtccagATGTGCCGTGCCCTTGCTTACATCCATCGTGTTGTCGGTGTGTGTCACCGTGATATTAAACCTCAAAATCTACTG

Basic information

species Zea mays
transcript GRMZM2G109624_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 5
gtttgtgatgatgttctgcttcattccagattccacctatcagattttttttttcaagaagtttagattcattggttggtatggaatgaacattaggaatgatcggttattccttcttgtccagATGTGCCGTGCCCTTGCTTACATCCATCGTGTTGTCGGTGTGTGTCACCGTGATATTAAACCTCAAAATCTACTG
              ||||  | | |    |||  | || |    |   |  ||||||   ||| | || ||| | ||   | | |||    ||| |   | ||  ||| | |  | ||    ||||||||||||||||||| || |||||||||||||| ||||| || || || ||||||||||||||||||||||||
-------------gtctgtataagttataattttagcttt---gtagatcatttcaaactgtt-aaatccat-gattctaaagaaat---tatttgttctaatgtgttttactatttttcatagATGTGCCGTGCCCTTGCATATATCCATCGTGTTGTTGGTGTCTGCCATCGAGATATTAAACCTCAAAATCTACTG
















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: 477

ACTTGAATTCGTATCTGAGACAGTTTATCGTGTTGCCAAATACTACAACCGGATGAACCAGCGTGTACCCATATTATATGTTAAGTTATATGCATATCAGgtttgtgatg ... tcttgtccagATGTGCCGTGCCCTTGCTTACATCCATCGTGTTGTCGGTGTGTGTCACCGTGATATTAAACCTCAAAATCTACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

ACTTGAATTCGTATCTGAGACAGTTTATCGTGTTGCCAAATACTACAACCGGATGAACCAGCGTGTACCCATATTATATGTTAAGTTATATGCATATCAGgtttgtgatg ... tcttgtccagATGTGCCGTGCCCTTGCTTACATCCATCGTGTTGTCGGTGTGTGTCACCGTGATATTAAACCTCAAAATCTACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

ACTTGAATTCGTATCTGAGACAGTTTATCGTGTTGCCAAATACTACAACCGGATGAACCAGCGTGTACCCATATTATATGTTAAGTTATATGCATATCAGgtttgtgatg ... tcttgtccagATGTGCCGTGCCCTTGCTTACATCCATCGTGTTGTCGGTGTGTGTCACCGTGATATTAAACCTCAAAATCTACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

ACTTGAATTCGTATCTGAGACAGTTTATCGTGTTGCCAAATACTACAACCGGATGAACCAGCGTGTACCCATATTATATGTTAAGTTATATGCATATCAGgtttgtgatg ... tcttgtccagATGTGCCGTGCCCTTGCTTACATCCATCGTGTTGTCGGTGTGTGTCACCGTGATATTAAACCTCAAAATCTACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattggttggtatggaatgaacattaggaatgatcggttattccttcttgtccagATGTGCCGTGCCCTTGCTTACATCCATCGTGTTGTCGGTGTGTGTCACCGTGATATTAAACCTCAAAATCTACTG
                                     ttattccttcttgtcc  CT-rich tract
                   aacatta  TA-rich tract