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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcagtctgaagtattgatgttaatgattatgataccttgatcatattggaacttaagtattaatgcattggcagGTGGTTAATTGTAAGGATGACCTTGCACAATTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGACGAATACCATTTACAAACATTGGAAACGTTAT

Basic information

species Zea mays
transcript GRMZM5G844195_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 7
gtttgcagtctgaagtattgatgttaatgattatgataccttgatcatattggaa-cttaagtattaatgcattggcagGTGGTTAATTGTAAGGATGACCTTGCACAATTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGACGAATACCATTTACAAACATTGGAAACGTTAT
|| |||| |  ||  | ||||        |  ||||| || ||||  || ||||| || ||| |  |||  |||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| || |
gtctgcaattagatttgttgacaaattataaaatgat-ccatgattctactggaagctgaagaagaaatatattggcagGTGGTTAATTGTAAGGATGAACTTGCACAATTCTACCTGATGGACTGCATAATACAAGTCTTTCCAGACGAATACCATTTACAGACATTGGAAACATTGT

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 8
--------------gtttgcagtctgaagtattgatgttaa-tgattatgataccttgat--catattggaacttaagtatt--aat--gcattggcagGTGGTTAATTGTAAGGATGACCTTGCACAATTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGACGAATACCATTTACAAACATTGGAAACGTTAT
               ||| |   |  || ||| | | ||   | ||| | |  |||||||   ||| ||   || |  | ||  |||  || |   ||||| || |||||||| ||||| ||||| ||||| || || ||||| ||||||||||| || ||||| || || |||||||| || ||| | || || || |
gtctaataaagtacattttctccccaaaatatagtttttctcttattgtaac-ccttgatgttatactgtctctcagctgtttaaattggcttgaacagGTTGTCAATTGTAAAGATGAGCTTGCCCAATTTTATCTTATGGAGTGCATAATCCAGGTTTTTCCCGATGAGTACCATTTGCAGACACTTGAGACTTTGT

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 7
--------------gtttgcagtctgaagtattgatgttaa-tgattatgataccttgat--catattggaacttaagtatt--aat--gcattggcagGTGGTTAATTGTAAGGATGACCTTGCACAATTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGACGAATACCATTTACAAACATTGGAAACGTTAT
               ||| |   |  || |||   | ||   | ||| | |  |||||||   ||||||   || |  | ||  |||  || |  |||||| || |||||||| ||||| ||||| ||||| || || ||||| ||||||||||| || |||||||| || |||||||| || ||| | || || || |
gtctaataaagtacattttctccccaaaatataatttttctcttattgtaac-ccttgatgttatattgtctctcagctgtttaaattggcttgagcagGTTGTCAATTGTAAAGATGAGCTTGCCCAATTTTATCTTATGGAGTGCATAATCCAGGTTTTTCCAGATGAGTACCATTTGCAGACACTTGAGACTTTGT

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 7
------gtttgcagtctgaagtattgatgttaatgattatgataccttgatcatattgg-aacttaagtatta--atgcattggcagGTGGTTAATTGTAAGGATGACCTTGCACAATTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGACGAATACCATTTACAAACATTGGAAACGTTAT
       ||| |  || |      |  | | |      |   | || |   ||| |||  ||||   || | |  |||  ||   |||| || || ||||||||||| |||||||| | |||||| ||||| ||||| || ||||||||||| || || |  ||  | |||||  | ||    ||||
gtctggtttttctctccgtttagatagtttcagcatccaaccttccgtctacatGTTGTCAACTATTGTCTCACTATGTCTTAAAAGGTTGTCAACTGTAAGGATGAACTTGCACAGTGCTACCTTATGGATTGCATTATTCAAGTCTTTCCTGATGATTTTCACCTTCAAACTCTCGATGTATTAT

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: 143

GTAGGCAAAAACCTTCATGTTCTAGGCCAGATTGACGGCGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAGgtttgcagtc ... gcattggcagGTGGTTAATTGTAAGGATGACCTTGCACAATTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGACGAATACCATTTACAAACATTGGAAACGTTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 166

GTAGGCAAAAACCTTCATGTTCTAGGCCAGATTGACGGCGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAGgtttgcagtc ... gcattggcagGTGGTTAATTGTAAGGATGACCTTGCACAATTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGACGAATACCATTTACAAACATTGGAAACGTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

GTAGGCAAAAACCTTCATGTTCTAGGCCAGATTGACGGCGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAGgtttgcagtc ... gcattggcagGTGGTTAATTGTAAGGATGACCTTGCACAATTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGACGAATACCATTTACAAACATTGGAAACGTTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 176

GTAGGCAAAAACCTTCATGTTCTAGGCCAGATTGACGGCGTTGACCTTGATATGTACAAAGAAACTGTTCTTCCAAGGATATTAGAGCAGgtttgcagtc ... gcattggcagGTGGTTAATTGTAAGGATGACCTTGCACAATTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGACGAATACCATTTACAAACATTGGAAACGTTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatgattatgataccttgatcatattggaacttaagtattaatgcattggcagGTGGTTAATTGTAAGGATGACCTTGCACAATTCTACCTGATGGACTGCATAATCCAAGTCTTTCCAGACGAATACCATTTACAAACATTGGAAACGTTAT
                                      tattaat  putative branch site (score: 176)
                              aacttaagtattaat  TA-rich tract