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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggcaattggtttcttttcttgcaatcatgaaatgtactgttttgctttgcccttgtaatactaatattttgtcccttttctaattattttcagGTTTCTGACCTTAAGCGGAACCTGAACATTGTTAATTCTTCAGCAGAAGAG

Basic information

species Zea mays
transcript AC197714.3_FGT005
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC197714.3_FGT005 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g17820.2 (Oryza sativa), 3'ss of exon 8
gtttggcaattggttt-cttttcttgcaatcatgaaatgtactgttttgctttgcccttgtaatactaatattttgtccctttt---ctaattattttcagGTTTCTGACCTTAAGCGGAACCTGAACATTGTTAATTCTTCAGCAGAAGAG
||  | ||| || ||| ||| | |||| |  | ||| |||  | ||||| || |||||| |  || |   | ||  |   |      ||| || | | |||||||||||||||||| ||| |||||||||||| || ||||| || ||||||
gtaagacaagtgatttacttattttgctactaagaactgtgatcttttggttggcccttttggtatttgaagttcatttttcccaaactacttttgtgcagGTTTCTGACCTTAAGAGGAGCCTGAACATTGTCAACTCTTCCGCGGAAGAG
















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), 42 (downstream exon)
Score: 120

TTCTTTATGGAGCTTATGAAATTACCACGTGTAGAATCTAAGCTGAGAGTTTTCTCATTTAAGATTCAATTCCGTTCCCAGgtttggcaat ... ttattttcagGTTTCTGACCTTAAGCGGAACCTGAACATTGTTAATTCTTCAGCAGAAGAG


Block sizes: 47 (upstream exon), 33 (downstream exon)
Score: 11

TTCTTTATGGAGCTTATGAAATTACCACGTGTAGAATCTAAGCTGAGAGTTTTCTCATTTAAGATTCAATTCCGTTCCCAGgtttggcaat ... ttattttcagGTTTCTGACCTTAAGCGGAACCTGAACATTGTTAATTCTTCAGCAGAAGAG


Block sizes: 25 (upstream exon), 31 (downstream exon)
Score: 11

TTCTTTATGGAGCTTATGAAATTACCACGTGTAGAATCTAAGCTGAGAGTTTTCTCATTTAAGATTCAATTCCGTTCCCAGgtttggcaat ... ttattttcagGTTTCTGACCTTAAGCGGAACCTGAACATTGTTAATTCTTCAGCAGAAGAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 107

TTCTTTATGGAGCTTATGAAATTACCACGTGTAGAATCTAAGCTGAGAGTTTTCTCATTTAAGATTCAATTCCGTTCCCAGgtttggcaat ... ttattttcagGTTTCTGACCTTAAGCGGAACCTGAACATTGTTAATTCTTCAGCAGAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgctttgcccttgtaatactaatattttgtcccttttctaattattttcagGTTTCTGACCTTAAGCGGAACCTGAACATTGTTAATTCTTCAGCAGAAGAG
                                 tcccttttctaatt  CT-rich tract
              ttgtaatactaatatt  TA-rich tract