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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagactttccttttcgtaacaggcatcattgtccaatcttgaaattttttactgctttcaagttccagcagtagtttccatttagcaatttttttgtaagctctaattggctccaatgaaagatttccatttatttttaagcagATTGGACATCAGCAGCTTGCACTTCAGAACTTGTATTCGGCTGACAGAGGGGTGAAACATAAAAACCTATCTGTCCTTTCAACTATTGCTGTGCTTCCTT

Basic information

species Zea mays
transcript GRMZM2G118641_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118641_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os01g22390.2 (Oryza sativa), 3'ss of exon 16
-----------gtaagactttc-cttttcgtaacaggcatcattgtccaatcttgaaattttttactgct-ttcaagttccagcagtagtttccatttagcaatttttttgtaagctctaattggctccaatgaaag--att-tccatttatttttaa--------gcagATTGGACATCAGCAGCTTGCACTTCAGAACTTGTATTCGGCTGACAGAGGGGTGAAACATAAAAACCTATCTGTCCTTTCAACTATTGCTGTGCTTCCTT
            ||| | |  | | |    | ||| | ||||| |   ||  |||| ||||   || |   |  | || ||   || |  ||      |     | | ||| ||  |   ||||| ||| |   |||  ||  || || |||| | ||        |||||||||||||||||||||  || ||||| || | |||||| ||||  |||| |||||| | |||||| | ||||| ||||| |||||| ||||||||||||
gtatgtactttttaatattcacgcctccaattacatg-atcatgga--aactttgatatttggcacagtaatataggtccctttagcaagttttggacattgtgtgtgttggaa--ttcgattggttcccacagaagtaatcgtcgatgtattgtcaatctatcatgcagATTGGACATCAGCAGCTCACATTTCAGTACCTCTATTCGTCTGATCGAGGAGTGAAATACAAAAACATGTCTGTTCTTTCGACTATTTCTGTGCTTCCTT
















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: 35 (upstream exon), 49 (downstream exon)
Score: 40

TTCAGACGGCATTTCCAACTTCTCTGTGTGGGGTCAGGACGTGGTATCAATTTCAAGGAACAAAATTGCACTAACTTCCCTGTCGAGACCAGAAAGTGAAgtaagacttt ... ttttaagcagATTGGACATCAGCAGCTTGCACTTCAGAACTTGTATTCGGCTGACAGAGGGGTGAAACATAAAAACCTATCTGTCCTTTCAACTATTGCTGTGCTTCCTT


Block sizes: 35 (upstream exon), 44 (downstream exon)
Score: 13

TTCAGACGGCATTTCCAACTTCTCTGTGTGGGGTCAGGACGTGGTATCAATTTCAAGGAACAAAATTGCACTAACTTCCCTGTCGAGACCAGAAAGTGAAgtaagacttt ... ttttaagcagATTGGACATCAGCAGCTTGCACTTCAGAACTTGTATTCGGCTGACAGAGGGGTGAAACATAAAAACCTATCTGTCCTTTCAACTATTGCTGTGCTTCCTT


Block sizes: 35 (upstream exon), 30 (downstream exon)
Score: 9

TTCAGACGGCATTTCCAACTTCTCTGTGTGGGGTCAGGACGTGGTATCAATTTCAAGGAACAAAATTGCACTAACTTCCCTGTCGAGACCAGAAAGTGAAgtaagacttt ... ttttaagcagATTGGACATCAGCAGCTTGCACTTCAGAACTTGTATTCGGCTGACAGAGGGGTGAAACATAAAAACCTATCTGTCCTTTCAACTATTGCTGTGCTTCCTT


Block sizes: 35 (upstream exon), 36 (downstream exon)
Score: 17

TTCAGACGGCATTTCCAACTTCTCTGTGTGGGGTCAGGACGTGGTATCAATTTCAAGGAACAAAATTGCACTAACTTCCCTGTCGAGACCAGAAAGTGAAgtaagacttt ... ttttaagcagATTGGACATCAGCAGCTTGCACTTCAGAACTTGTATTCGGCTGACAGAGGGGTGAAACATAAAAACCTATCTGTCCTTTCAACTATTGCTGTGCTTCCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgtaagctctaattggctccaatgaaagatttccatttatttttaagcagATTGGACATCAGCAGCTTGCACTTCAGAACTTGTATTCGGCTGACAGAGGGGTGAAACATAAAAACCTATCTGTCCTTTCAACTATTGCTGTGCTTCCTT
           ctctaat  putative branch site (score: 17)
                                  tttccatttattttt  putative PPT
                             aaagatttccatttat  TA-rich tract