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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagctaccccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG

Basic information

species Zea mays
transcript GRMZM5G858094_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 7
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagctacccc----ccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
      ||| || | |  |  |  ||||     |    |  |       | |||| |||     || || | |    | || | |||||| ||| |||  || | || ||||||||||||||||||||||||||  |  | ||||||||||| ||||| ||||| ||||| |||||||||||| |||||||||| ||  | |||
-----gtttgttct-tcttgtagttatcaagagattgtttggattgcaagtgtttagtgcccatagttaactctggtctttctaacatgagtaactcaactttcttg-cagGTTCATAATGATGATGAGGTTAGGACATTATTTAAGCAAGTTCAAGGCGAAGTACCTGGTTCCCCAATATTTATCATGAGGCTAGCTGCTCAG

upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 3
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagct-accccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
   ||| | | ||  |     ||| |     |||    |||||  ||   | |||||| ||    | |   |    ||| || |  |  |      |    ||   |||||||||||||||||||||| || ||  |||| |||||||| ||||||||||| || || || || |||||| | |||| | |||||||||||
---tgcataaatacctataagaacaa-----gaaactttgtgccaatcttattttggtatgatttgtttggcaaagtttagaaactaacaggcatatggatcttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCAGGTTCTCCCATATTTATAATGAAGGTTGCATCCCAG

upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 3
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagct-accccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
   ||| | | ||  |     ||| |     |||    |||||  ||   | |||||| ||    | |   |    ||| || |  | ||      |     |   |||||||||||||||||||||| || ||  |||| |||||||| ||||||||||| || || || || |||||| | |||| | |||||||||||
---tgcataaatacctataagaacaa-----gaaactttgtgccaatcttattttggtatgatttgtttggcaaagtttagaaactaataggcatatggattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG

upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagctaccccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
                       ||   | || |||  ||     | ||    ||  |      ||| |        ||    |  ||   |||||||    |  ||||||||||||||||||||||||| || || || |||||||| |||||||| ||||| ||||| || |||||| | |||| | |||| || |||
---------------------gtctgcttctgtagatatg-----actgtcactttttccactaagccaaagtgtacttattgtagtttt-tcattttg---gtaagGTTCATAATGATGATGAGGTTAGGGCTCTATTCAAGCAAGTTCAAGGTGAGGTCCCGGGCTCGCCGATATTTATAATGAAGGTTGCTTCACAG

upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagctaccccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
                       |    | || |||  | ||| | || || | |||  |  |  | |  |    |    || |  |    |  |||    |   ||||||||||||||||||||||||| || || || |||||||| || ||||| ||||| ||||| ||||||||  | |||| | |||| || |||
---------------------gtcagcttctgtaga--tatgc-cttttgattgtggactaagccgattactatataagtacttattctggt--tttaaatttatagGTTCATAATGATGATGAGGTTAGGGCTCTATTCAAGCAAGTTCAGGGTGAGGTCCCAGGCTCACCAATATTCATAATGAAGGTTGCGTCACAG

upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagctaccccccttttgacatga-------ttaaatcattttcc--ctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
                ||    ||    | ||  ||  ||   |  ||||| | |  ||         |   | |   ||| ||||        | | |||||||    ||   ||||||||||||||||||| || |  ||  |||| |||||||| ||||||||||| ||||||||||| |||||    |||| | |||| ||||||
----------------gaagtcacgggttatgttgagatgattagtttggactgtcatgattttcctaatttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 293

CGTTACTACCACAGAGGAAGCAGTTGCAAGTTGTCAAGTGGTTGGTTATCCTGCCATGATTAAGGCATCCTGGGGAGGTGGTGGTAAAGGAATAAGAAAGgtgtgcttta ... tccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 284

CGTTACTACCACAGAGGAAGCAGTTGCAAGTTGTCAAGTGGTTGGTTATCCTGCCATGATTAAGGCATCCTGGGGAGGTGGTGGTAAAGGAATAAGAAAGgtgtgcttta ... tccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 101

CGTTACTACCACAGAGGAAGCAGTTGCAAGTTGTCAAGTGGTTGGTTATCCTGCCATGATTAAGGCATCCTGGGGAGGTGGTGGTAAAGGAATAAGAAAGgtgtgcttta ... tccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 640

CGTTACTACCACAGAGGAAGCAGTTGCAAGTTGTCAAGTGGTTGGTTATCCTGCCATGATTAAGGCATCCTGGGGAGGTGGTGGTAAAGGAATAAGAAAGgtgtgcttta ... tccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtgtggggagctaccccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG
                       ttttgac  putative branch site (score: 640)
                                       tcattttccct  putative PPT
                              atgattaaatcatttt  TA-rich tract