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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacactctggattgttggagtattagcttatttatttctgatcgttttagatgctagttaacttggtcttaaaaattcagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACAT

Basic information

species Zea mays
transcript GRMZM2G120951_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120951_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 4
gta-taacac----tctggattgttggagtattagcttatttatttctgatcgttttaga-tgctagttaacttggtctt--aaaaattcagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACAT
||| | ||||    | | || |  |     |  | ||  ||| ||| ||  | ||  | | |  || |||||||||| |   ||||||  |||||||||||||||| ||||||||||| |||||||| ||||||||||| ||||||| 
gtaatgacacctcattttgactactacgagagaaactgttttctttttgccctttccaaaattttaattaacttggtttatgaaaaatgtagGTTATGGATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACAC

upper sequence: GRMZM2G120951_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 4
gtataacactctggattgttg--gagtattagcttatt--tatttctgatcgttttagatgctagttaacttggtcttaaaaattcagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACAT
||||     |  |  || ||   ||||    | | |||  || | || ||  ||||  ||| |  || |||   | |      | ||||||||||||||||| ||||| || || ||||| || ||||||||||    |||   
gtatgttgttgagtcttattcttgagtgcatgttcattattactact-attattttgaatgatgattcact--atttcctttgtgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA

upper sequence: GRMZM2G120951_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 4
gtataacactctggattgttg--gagtattagcttatt--tatttctgatcgttttagatgctagttaacttggtcttaaaaattcagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACAT
||||     |  |  || ||   |||| || | | |||  |||  || ||  ||||  ||| |  ||  |    | |      | ||||||||||||||||| ||||| || || ||||| || ||||||||||    |||   
gtatgttgttgagtcttattcttgagtgtttgttcattattatgact-attattttgaatgatgatt--ccatatttcctttgtgcagGTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCA

upper sequence: GRMZM2G120951_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------gtataa---cactctggattgttggagtattagctta-tttatttctgatcgttttaga-tgctagttaacttgg---tcttaaaaatt-cagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACAT
                            ||| |    |   |||     ||  |  ||   ||| | | |||||  |   |||||| ||   ||    | |     || ||   || ||||||||||| ||||| ||||| ||  |||||||||| ||||||||||| ||||||| 
gtatgctatcatttgctgtcttgttggttatgaatttatggtggtcaactgtggagtttctttagtctgtttctccttaatttagaatgtctgtgtgatagaaaacctgaatggttgcagGTTATGGACATGCTTGGACCAAGCTTGTGGGATGTTTGGAATAATAACTCTCACAC

upper sequence: GRMZM2G120951_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 4
------------------gtataacactctggatt--gttggagtattagcttatttatttctgatcgttttagatgctagttaacttggtcttaaaa---attcagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACAT
                   | |     |   ||||   |   ||| | | ||   || | | |     |||   |||    |  |      |||  ||   || ||||||||||||||||| ||||| ||| |||||||||| |||||||| || || |||| 
gtatgtgccaagtattttatgtgttttttatgattttataacagtgtgatctagcttttctttatggatttagaatgacgatggagaaaacctttcaatgcatacagGTTATGGATATGCTTGGACCTAGTTTGTGGGATGTTTGGAATAACAACTCACACAC

upper sequence: GRMZM2G120951_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S208_76V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------------------------------gtataacactctggattgttggagtattagcttatttatttctgatcgttttagatgctagttaacttggtcttaaaaattcagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAAT---AAATCTCACAT--
                                                                                           |  |||       ||  ||    ||||    ||||||||| |  |  |||||        |  |||| || || |   |  ||||||| |||||| ||||||| ||||| ||||||||||||||   |   | |||   |    
gtcgataaggtgactactacgtcatggtgaatcatctattgaattgttgtagtccaagcagaccttcagttttcatgtagtcgtcttcttttcaaacttctctcatgatttatttatttatgtatttatttat--ttattttaatctgatttcgacttcgtattcatgctgtagGTTATAGATATGGTCGGACCAAGTCTCTGGGATGTCTGGAACTCTTCGAGATCAAGCGCAA

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: 44 (upstream exon), 46 (downstream exon)
Score: 39

CGCCATTGGTGGCATTCATGGGTTTCCCCGAGTCCACTACAAAGGACGCCAAGGGGATTACTTTGTTATGgtataacact ... aaaaattcagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 20

CGCCATTGGTGGCATTCATGGGTTTCCCCGAGTCCACTACAAAGGACGCCAAGGGGATTACTTTGTTATGgtataacact ... aaaaattcagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 20

CGCCATTGGTGGCATTCATGGGTTTCCCCGAGTCCACTACAAAGGACGCCAAGGGGATTACTTTGTTATGgtataacact ... aaaaattcagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 13

CGCCATTGGTGGCATTCATGGGTTTCCCCGAGTCCACTACAAAGGACGCCAAGGGGATTACTTTGTTATGgtataacact ... aaaaattcagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttatttatttctgatcgttttagatgctagttaacttggtcttaaaaattcagGTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACAT
                              agttaac  putative branch site (score: 13)
                                         tcttaaaaatt  TA-rich tract