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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatatccatatccaaccatgtttcagtttgcttactctgtgtaatggatctactgtttatggggtgaaaaacatcgatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTATCAATGTTCTGCTGTCAAAAACTGCCATTGCACCAGTCAACGAAAC

Basic information

species Zea mays
transcript GRMZM2G044246_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
gtaatatatccatatccaaccatgtttcagttt-gcttactctgtgtaatggatctactgtttatggggtgaaaaacatcgatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTATCAATGTTCTGCTGTCAAAAACTGCCATTGCACCAGTCAACGAAAC
            ||      |  ||   | ||  || ||  ||      | |||| |  ||  || || | | ||||  |  ||   ||||| |||||||||||||||| ||| |||| |||||||||||||||||||||||| |||  || ||||  ||||||||||| |||||||| || |||  |||
-----------gtaagtggtcgagtgataattaagcatatact------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC

upper sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G14050.1 (Glycine max), 3'ss of exon 6
gtaatatatccatatccaaccatgtttcagtttgcttactctgtgtaatggatctactgtttatggggtgaaaaacatcgatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTATCAATGTTCTGCTGTCAAAAACTGCCATTGCACCAGTCAACGAAAC
||||  |  |     ||||  |||||   | |    | || |   || |  ||  |   || |  |  | ||     |        |||| ||||||||||||||| |||  ||||| || ||| ||||||||||||| ||  | |  || || |  ||||||||||||||||||||||||||   |||
gtaacgttgctg---ccaa--atgtt---gctcatatgctgtaattatt--attgatatttcactgtattaagggtgttatgcctgcagAAGGTGCAAGGGCTGCTTTGAGCCTGTCTGGTACCATGCTTGGATATTACCCACTGAGAGTGCTACCTTCAAAAACTGCCATTGCACCAGTCAATCCAAC

upper sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G40760.1 (Glycine max), 3'ss of exon 6
gtaatatatccatatccaaccatgtttcagtttgcttactctgtgtaatggatctactgtttatggggtgaaaaacatcgatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTATCAATGTTCTGCTGTCAAAAACTGCCATTGCACCAGTCAACGAAAC
|||| ||  |||   ||||   | || ||  ||  | | |    || || ||  |    ||    |  | || |   | |   |  |||| ||||||||||||||| |||| ||||| |||||| ||||||||||||| ||  | |  || || |  || |||||||| ||||| || || ||   |||
gtaacatgacca---ccaaatgt-ttgcaactttgtaatt----gttattgacat----ttctctgtattaacagtgttgtgcttgcagATGGTGCAAGGGCTGCTTTGAACCTGTCTGGAACCATGCTTGGATATTACCCGTTGAGAGTACTACCTTCGAAAACTGCTATTGCCCCTGTTAATCCAAC

upper sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G35640.1 (Glycine max), 3'ss of exon 5
gtaatatatccatatccaaccatgtttcagtttgcttactctgtgtaatggatctactgtttatggggtgaaaaacatcgatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTATCAATGTTCTGCTGTCAAAAACTGCCATTGCACCAGTCAACGAAAC
|||| ||  ||      |   |||  ||  | || ||| |           ||  ||  || |  |  | || |   | |       ||| ||||||||||||||| |||| ||||| |||||| ||||||||||||| ||  | |  || || |  ||||||||||| ||||  || || ||   |||
gtaacatgaccgc-caaatgtatgcatctttgtgattatt-----------attaacatttcactgtattaacagtgttgtgcctgtagAAGGTGCAAGGGCTGCTTTGAACCTGTCTGGAACCATGCTTGGATATTACCCGTTGAGAGTGCTACCTTCAAAAACTGCTATTGTCCCTGTTAATCCAAC

upper sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G14030.2 (Glycine max), 3'ss of exon 6
gtaatatatccatatccaaccatgtttcagtttgcttactctgtgtaatggatctactgtttatggggtgaaaaacatcgatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTATCAATGTTCTGCTGTCAAAAACTGCCATTGCACCAGTCAACGAAAC
|||| ||  ||      |   |||  ||  | || ||| |           ||  ||  || |  |  | || |   | |      |||| ||||||||||||||| |||| ||||| |||||| ||||||||||||| ||  | |  || || |  ||||||||||| ||||| || || ||   |||
gtaacatgaccgc-caaatgtatgcatctttgtgattatt-----------attaacatttcactgtattaacagtgttgtgcctgcagAAGGTGCAAGGGCTGCTTTGAACCTGTCTGGAACCATGCTTGGATATTACCCGTTGAGAGTGCTACCTTCAAAAACTGCTATTGCCCCTGTTAATCCAAC

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: 47 (upstream exon), 49 (downstream exon)
Score: 99

GTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGGgtaatatatc ... gatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTATCAATGTTCTGCTGTCAAAAACTGCCATTGCACCAGTCAACGAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

GTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGGgtaatatatc ... gatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTATCAATGTTCTGCTGTCAAAAACTGCCATTGCACCAGTCAACGAAAC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 124

GTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGGgtaatatatc ... gatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTATCAATGTTCTGCTGTCAAAAACTGCCATTGCACCAGTCAACGAAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 157

GTTGTGGACTGTCGCATGTGTGGGGACCCAAATTCAGTCCTTAGGTTTGCTTTCATAGAGTTCACTGATGAGGgtaatatatc ... gatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTATCAATGTTCTGCTGTCAAAAACTGCCATTGCACCAGTCAACGAAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttactctgtgtaatggatctactgtttatggggtgaaaaacatcgatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTATCAATGTTCTGCTGTCAAAAACTGCCATTGCACCAGTCAACGAAAC
 tgcttac  putative branch site (score: 157)
                                    aaaaacat  TA-rich tract