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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagtcttgctctaagttcatttaacatagaaccatattattttaaagggatgctatatgtgaatgtgcagATCTTCGAATGGTTGGGTAGCATGCCTGTTGAATTGGAGGGCTACATTCGTCCGGGTTGTATTATTTTAACTGTATTTATTGCAATGCCACAGCATATGT

Basic information

species Zea mays
transcript GRMZM2G109354_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109354_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g33810.1 (Oryza sativa), 3'ss of exon 4
--gtatagtcttgctctaagttcatt--taacatagaaccat------------attattttaaagg-gatgctatatgtgaa-tgtgcagATCTTCGAATGGTTGGGTAGCATGCCTGTTGAATTGGAGGGCTACATTCGTCCGGGTTGTATTATTTTAACTGTATTTATTGCAATGCCACAGCATATGT
   ||||  |  ||||||||||  |   || ||        |            ||| || | ||    |||| ||| || || | ||||||| || || ||| |   |||||||||||||||| |||||||||| |||||||| |||||||  ||||||||||||||| ||||||||||||| |||||||
gtatataaccaggctctaagtttctcaatagcacgctgttttcatgcccaaaagattgttctgaactcaatgccatacgtaaaatatgcagATATTTGAGTGGCTTTCTAGCATGCCTGTTGAACTGGAGGGCTATATTCGTCCTGGTTGTACAATTTTAACTGTATTTGTTGCAATGCCACAACATATGT

upper sequence: GRMZM2G109354_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G18830.3 (Arabidopsis thaliana), 3'ss of exon 4
--------------------gtatagtct--tgctctaagttcat-ttaacat----agaaccatattattttaaagggatgctat--atgtgaatgtgcagATCTTCGAATGGTTGGGTAGCATGCCTGTTGAATTGGAGGGCTACATTCGTCCGGGTTGTATTATTTTAACTGTATTTATTGCAATGCCACAGCATATGT
                     || ||| |  || || |||   || || || |    |||| |  |      |||     ||| ||  || ||||| ||||||| ||  |||||||||  | ||||||||||||  |||||||||| || || || || ||||  ||||| ||||| ||||| ||||||||| ||  |||||
gtattctcaagaattatatattacagtttagtgttcaaagactatgtttaccttctcagaatctcaaagaactaatatcttgcgattaatttgaatttgcagATATTTCAATGGTTGGCCAACATGCCTGTTGAGCTGGAGGGCTATATCCGCCCAGGATGTACAATTTTGACTGTCTTTATAGCAATGCCAGAGATTATGT

upper sequence: GRMZM2G109354_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0020g02160.t01 (Vitis vinifera), 3'ss of exon 4
------------------------gtatagtcttgctctaag--------ttcatttaacatagaaccat----attattttaaagggatgctatatgtgaatgtgcagATCTTCGAATGGTTGGGTAGCATGCCTGTTGAATTGGAGGGCTACATTCGTCCGGGTTGTATTATTTTAACTGTATTTATTGCAATGCCACAGCATATGT
                        || |||| ||  | | ||        ||  | |||   |||   |     | ||| ||||     ||||  |||||  | | ||||| ||| | ||||||| |||||||||| |||| ||||||||||| || ||||| || ||||| || |||||  | ||||||||||||||| ||  |||||
gtattttaaaggattattattacagtttagtatttatatgagaataaatgtttttataagtcagagataccaggaatatattaacacactgctcaatgtg--tttacagATTTTCCAGTGGTTGGCTAGCATGCCTATTGAGTTGGAGGGCTATATCCGTCCTGGGTGTATCATCTTAACAATTTTTATTGCAATGCCAAAGTTTATGT

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: 43 (upstream exon), 44 (downstream exon)
Score: 43

TGTCCAACAGGGCGCATCTCATTCAAGTTGTATGATTGGAATCCTGCAGAATTTCCTCGACGACTACGACACCAGgtatagtctt ... gaatgtgcagATCTTCGAATGGTTGGGTAGCATGCCTGTTGAATTGGAGGGCTACATTCGTCCGGGTTGTATTATTTTAACTGTATTTATTGCAATGCCACAGCATATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 43

TGTCCAACAGGGCGCATCTCATTCAAGTTGTATGATTGGAATCCTGCAGAATTTCCTCGACGACTACGACACCAGgtatagtctt ... gaatgtgcagATCTTCGAATGGTTGGGTAGCATGCCTGTTGAATTGGAGGGCTACATTCGTCCGGGTTGTATTATTTTAACTGTATTTATTGCAATGCCACAGCATATGT


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 72

TGTCCAACAGGGCGCATCTCATTCAAGTTGTATGATTGGAATCCTGCAGAATTTCCTCGACGACTACGACACCAGgtatagtctt ... gaatgtgcagATCTTCGAATGGTTGGGTAGCATGCCTGTTGAATTGGAGGGCTACATTCGTCCGGGTTGTATTATTTTAACTGTATTTATTGCAATGCCACAGCATATGT


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 51

TGTCCAACAGGGCGCATCTCATTCAAGTTGTATGATTGGAATCCTGCAGAATTTCCTCGACGACTACGACACCAGgtatagtctt ... gaatgtgcagATCTTCGAATGGTTGGGTAGCATGCCTGTTGAATTGGAGGGCTACATTCGTCCGGGTTGTATTATTTTAACTGTATTTATTGCAATGCCACAGCATATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttaacatagaaccatattattttaaagggatgctatatgtgaatgtgcagATCTTCGAATGGTTGGGTAGCATGCCTGTTGAATTGGAGGGCTACATTCGTCCGGGTTGTATTATTTTAACTGTATTTATTGCAATGCCACAGCATATGT
   atttaac  putative branch site (score: 51)
          atagaaccatattatt  TA-rich tract