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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaggtttaggaaattatctttcttttctgctcatggaagtgctggtttaatatttgaattcacaacaaccttaaatatatgtacttctaatgctttccttgaacatttttgaccagaaattgttgttctataatttctcatttaagttccttttttactagtataatggtgtcaacatatttcagGCTGGTCTTGTGGCAGCTGATATAGAGATTTCTGATTGGTTACGACGCAACTACTCTGACAAGTGTATTCTACTTGCTGTCAATAAGTGTGAATCTCCAC

Basic information

species Zea mays
transcript GRMZM2G302233_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G302233_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0004g02070.t01 (Vitis vinifera), 3'ss of exon 5
gcaggtttaggaaattatctttcttttctgctcatggaagtgctggtttaatatttgaattcacaacaaccttaaatatatgtacttctaatgctttccttgaacatttttgaccagaaattgttgttctataatttctcatttaagttccttttttactagtataatggtgtcaaca-tattt--cagGCTGGTCTTGTGGCAGCTGATATAGAGATTTCTGATTGGTTACGACGCAACTACTCTGACAAGTGTATTCTACTTGCTGTCAATAAGTGTGAATCTCCAC
                                                                                      ||| ||   || |||||        |   | |  || |  |  ||  |   |     ||  ||| | | ||| ||  | | |  ||| || | || |   ||||| |||||    ||||||||| | || ||  | |||||| ||||    || |||||  ||||||||||| | |||||||| || ||||||||||||||| 
--------------------------------------------------------------------------------------tcttat---tttcttgagtgagcaagcaaatatcttctcatgttagtaaaacagtaatatcttcttgtgttagtaaaacagtaatgtaaaaaatactgaacagGCAGGTCTATCAGCAGCTGATGTGGAAATAGCAGATTGGCTACGTAAAAATTACTCAAACAAGTGTATTGTTCTTGCTGTGAACAAGTGTGAATCTCCAA
















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: 257

TAGAGAAGCTGCTATTGCAAGGATGCCATCAATGATTGAAAAACAAGCAGTTGCAGCTGTTGATGAAGCATCCGTCATACTATTCGTTGTGGATGGTCAGgcaggtttag ... catatttcagGCTGGTCTTGTGGCAGCTGATATAGAGATTTCTGATTGGTTACGACGCAACTACTCTGACAAGTGTATTCTACTTGCTGTCAATAAGTGTGAATCTCCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 506

TAGAGAAGCTGCTATTGCAAGGATGCCATCAATGATTGAAAAACAAGCAGTTGCAGCTGTTGATGAAGCATCCGTCATACTATTCGTTGTGGATGGTCAGgcaggtttag ... catatttcagGCTGGTCTTGTGGCAGCTGATATAGAGATTTCTGATTGGTTACGACGCAACTACTCTGACAAGTGTATTCTACTTGCTGTCAATAAGTGTGAATCTCCAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 79

TAGAGAAGCTGCTATTGCAAGGATGCCATCAATGATTGAAAAACAAGCAGTTGCAGCTGTTGATGAAGCATCCGTCATACTATTCGTTGTGGATGGTCAGgcaggtttag ... catatttcagGCTGGTCTTGTGGCAGCTGATATAGAGATTTCTGATTGGTTACGACGCAACTACTCTGACAAGTGTATTCTACTTGCTGTCAATAAGTGTGAATCTCCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

TAGAGAAGCTGCTATTGCAAGGATGCCATCAATGATTGAAAAACAAGCAGTTGCAGCTGTTGATGAAGCATCCGTCATACTATTCGTTGTGGATGGTCAGgcaggtttag ... catatttcagGCTGGTCTTGTGGCAGCTGATATAGAGATTTCTGATTGGTTACGACGCAACTACTCTGACAAGTGTATTCTACTTGCTGTCAATAAGTGTGAATCTCCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttctcatttaagttccttttttactagtataatggtgtcaacatatttcagGCTGGTCTTGTGGCAGCTGATATAGAGATTTCTGATTGGTTACGACGCAACTACTCTGACAAGTGTATTCTACTTGCTGTCAATAAGTGTGAATCTCCAC
                    ttttttactagtataa  TA-rich tract