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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtttgttagttccttgctttcttgttcaactttagttgatcgcatgcaccgtctcagttttcatcagctgtgatgctcttgtgcctcttccagGTGAGGCTTGCCAAGATACAGGATGCTGGAGACGTGTCCAAAACATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTG

Basic information

species Zea mays
transcript AC209819.3_FGT007
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC209819.3_FGT007 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g39760.1 (Oryza sativa), 3'ss of exon 2
gttggtttgttagttccttgctttcttgttcaactttagttgatcgcatgcaccgtctcagttttcatcagctgtgatgctcttgtgcctcttccagGTGAGGCTTGCCAAGATACAGGATGCTGGAGACGTGTCCAAAACATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTG------
    |||  |       |||  || || || | ||||   ||||   |     | | | || | |  |||| ||| ||  | |  | |  |   |||||||| ||||||||||||  ||||| |||||| ||  | |  |||||||| || || ||||| |||||||||||||| ||||| || |||||||      
----gttaatggacgtattgtgttgtt-ttgatcttt---tgat-ataaattacattttagatatt-tcagatgtaatcatgtgttactgcaaacagGTGAGACTTGCCAAGATAGGGGATGGTGGAGATGTACCTACTACATTGCTAGGCGATCATGATGGAAGGGCTCACAAGTTGGCCATTGAGCCTGGCAGTC
















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 3 RNA-Seq libraries.


Block sizes: 11 (upstream exon), 39 (downstream exon)
Score: 3

ATTAGAGTTTCATTCAGGACATGGCGGCAATGTGTTCCAGGCACGGTTCATGCCCTGCTCAGACGATCGGACCATTGTCACTTGTGTTGCTGATGGCGAGgttggtttgt ... cctcttccagGTGAGGCTTGCCAAGATACAGGATGCTGGAGACGTGTCCAAAACATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTG


Block sizes: 12 (upstream exon), 38 (downstream exon)
Score: 1

ATTAGAGTTTCATTCAGGACATGGCGGCAATGTGTTCCAGGCACGGTTCATGCCCTGCTCAGACGATCGGACCATTGTCACTTGTGTTGCTGATGGCGAGgttggtttgt ... cctcttccagGTGAGGCTTGCCAAGATACAGGATGCTGGAGACGTGTCCAAAACATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTG


Block sizes: 11 (upstream exon), 40 (downstream exon)
Score: 5

ATTAGAGTTTCATTCAGGACATGGCGGCAATGTGTTCCAGGCACGGTTCATGCCCTGCTCAGACGATCGGACCATTGTCACTTGTGTTGCTGATGGCGAGgttggtttgt ... cctcttccagGTGAGGCTTGCCAAGATACAGGATGCTGGAGACGTGTCCAAAACATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgcatgcaccgtctcagttttcatcagctgtgatgctcttgtgcctcttccagGTGAGGCTTGCCAAGATACAGGATGCTGGAGACGTGTCCAAAACATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTG
 agttgat  putative branch site (score: 5)
                                     ctcttgtgcctcttcc  putative PPT
                   ttttcat  TA-rich tract