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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcaattcttactgtatcaagctgatcttctaatactttaaaatatggttaagaattacttgcaagctaagttgatgagttttcctctttaaattgcagGCACTGGATACATTTAATACAGCAGTAGTCTCACCAATATATTACGTGATGTTTACATCACTAACAATTATAGCTAGTGTGATAATGTTCAAG

Basic information

species Zea mays
transcript GRMZM2G104147_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104147_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 6
ttgcaattcttactgtatcaagctgatcttctaatactttaaaatatggttaagaattacttgcaagctaagttgatgagttttcctctttaaattgcagGCACTGGATACATTTAATACAGCAGTAGTCTCACCAATATATTACGTGATGTTTACATCACTAACAATTATAGCTAGTGTGATAATGTTCAAG
    ||    ||   |||  ||||    || |  ||   ||  | ||        ||||| |  | || |   | ||   |||  |||| | | ||||||||| |||| || |||||||||||||| ||||||||||||||||||||||||||||| |||||||||||| |||| |||||||||||||| |||
acagaacatgtagcttattgagctaccattattgtaacatatcacataagggcttattacattaacgcaatagtaattcttttatctctgtgacttgcagGCATTGGACACCTTTAATACAGCAGTTGTCTCACCAATATATTACGTGATGTTTACTTCACTAACAATTTTAGCCAGTGTGATAATGTTTAAG

upper sequence: GRMZM2G104147_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G71900.1 (Arabidopsis thaliana), 3'ss of exon 6
-----ttgcaattcttactgtatcaagctgatc--ttctaatactttaaaata--tggttaagaat---tacttgcaagctaagttgatgagtttt---cctctttaaattgcagGCACTGGATACATTTAATACAGCAGTAGTCTCACCAATATATTACGTGATGTTTACATCACTAACAATTATAGCTAGTGTGATAATGTTCAAG
     |   ||||       | ||| | | |||  ||  || ||||| |  |   |  |||    |   |  |||  |  |||     ||  ||||       ||| | |||||||| || |||||||| ||||||||  |||| || || ||||| ||||||||||| ||||| ||||| ||| | |||||||| || ||||| |||
gtaactattaattaagtgattttcaggataatcgattggaagactttgacgtgggtaattagatgtctatctttgttacttaaagaattgcattttgtattgttttcacttgcagGCTCTTGATACATTCAATACAGCTATAGTATCTCCTATATACTACGTGATGTTCACATCTCTAACTATTTTGGCTAGTGTCATCATGTTTAAG
















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: 35

AACATTCTCAGGAACAAATCAATTATTCTATCCTCAGACTTGGGCCTTTGCAGTAATTGTAGCTACCTGTGTGAGCACCCAAATTAACTATCTGAATAAGgtaattgttc ... taaattgcagGCACTGGATACATTTAATACAGCAGTAGTCTCACCAATATATTACGTGATGTTTACATCACTAACAATTATAGCTAGTGTGATAATGTTCAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 21

AACATTCTCAGGAACAAATCAATTATTCTATCCTCAGACTTGGGCCTTTGCAGTAATTGTAGCTACCTGTGTGAGCACCCAAATTAACTATCTGAATAAGgtaattgttc ... taaattgcagGCACTGGATACATTTAATACAGCAGTAGTCTCACCAATATATTACGTGATGTTTACATCACTAACAATTATAGCTAGTGTGATAATGTTCAAG


Block sizes: 47 (upstream exon), 38 (downstream exon)
Score: 7

AACATTCTCAGGAACAAATCAATTATTCTATCCTCAGACTTGGGCCTTTGCAGTAATTGTAGCTACCTGTGTGAGCACCCAAATTAACTATCTGAATAAGgtaattgttc ... taaattgcagGCACTGGATACATTTAATACAGCAGTAGTCTCACCAATATATTACGTGATGTTTACATCACTAACAATTATAGCTAGTGTGATAATGTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 107

AACATTCTCAGGAACAAATCAATTATTCTATCCTCAGACTTGGGCCTTTGCAGTAATTGTAGCTACCTGTGTGAGCACCCAAATTAACTATCTGAATAAGgtaattgttc ... taaattgcagGCACTGGATACATTTAATACAGCAGTAGTCTCACCAATATATTACGTGATGTTTACATCACTAACAATTATAGCTAGTGTGATAATGTTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggttaagaattacttgcaagctaagttgatgagttttcctctttaaattgcagGCACTGGATACATTTAATACAGCAGTAGTCTCACCAATATATTACGTGATGTTTACATCACTAACAATTATAGCTAGTGTGATAATGTTCAAG
                         agttgat  putative branch site (score: 107)
                                   ttttcctcttt  putative PPT
                                         tctttaaatt  TA-rich tract