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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggctgtgttttttctttacaatcgtattgcactgttccatgagctgttgttgcactgggatgccttgtttcatcaccatcctatgcttgtttaggcatgcttgtgcagatgcatgaagggtcctcttgtaatatttctctttaacttgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGAGTGTGACCATCTTGTGCATGAGGGGTTTGAAAGCACTGTAAGTTTACTTTGCCCTGCCAACCACATCGGT

Basic information

species Zea mays
transcript GRMZM2G135218_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135218_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 3
gtagggctgtgt-tttttctttacaatcgtattgcactgttccatgagctgt-tgttgca-ctgggatgccttgtttcatc-accatcctatgcttgtttaggcatgcttgtgcagatgcatgaagggtcctcttgtaatatttctctttaacttgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGAGTGTGACCATCTTGTGCATGAGGGGTTTGAAAGCACTGTAAGTTTACTTTGCCCTGCCAACCACATCGGT
||||||  |    || |||| |||  |    ||    ||  | |  |  ||  |||||   ||| |  |  |  |  |||| ||  | ||||| || |       |||||    ||||  | | ||  |  | |||| | |||| | ||| |  |||||||| || ||||| ||||| ||||||||||||||||||| ||||||||||||||||||||||||||||                                 
gtagggtagcacgttcttctctactgtttacttttgttg--caaatacttgcatgttgtgtctgtgcagagtactcacatccacatttctatgattatc---atgtgcttacttagattgacgtaga-tatttttgtgacatttatgtttgatgtgcagGAGACTGAAGAAAAAGCACTGGGTGATAGAGTGTGACCCTCTTGTGCATGAGGGGTTTGAAAGCACT---------------------------------
















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: 16 (upstream exon), 48 (downstream exon)
Score: 27

CAGCATTTGTGCAGCCACCAGCTGATCAAACACCAGATAGTTCTCCATATATTCGACCTGCATTTAAGCATGTGCTACGTCATCCTATAATAGAAAATGGgtagggctgt ... taacttgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGAGTGTGACCATCTTGTGCATGAGGGGTTTGAAAGCACTGTAAGTTTACTTTGCCCTGCCAACCACATCGGT


Block sizes: 16 (upstream exon), 47 (downstream exon)
Score: 12

CAGCATTTGTGCAGCCACCAGCTGATCAAACACCAGATAGTTCTCCATATATTCGACCTGCATTTAAGCATGTGCTACGTCATCCTATAATAGAAAATGGgtagggctgt ... taacttgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGAGTGTGACCATCTTGTGCATGAGGGGTTTGAAAGCACTGTAAGTTTACTTTGCCCTGCCAACCACATCGGT


Block sizes: 15 (upstream exon), 47 (downstream exon)
Score: 6

CAGCATTTGTGCAGCCACCAGCTGATCAAACACCAGATAGTTCTCCATATATTCGACCTGCATTTAAGCATGTGCTACGTCATCCTATAATAGAAAATGGgtagggctgt ... taacttgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGAGTGTGACCATCTTGTGCATGAGGGGTTTGAAAGCACTGTAAGTTTACTTTGCCCTGCCAACCACATCGGT


Block sizes: 10 (upstream exon), 46 (downstream exon)
Score: 9

CAGCATTTGTGCAGCCACCAGCTGATCAAACACCAGATAGTTCTCCATATATTCGACCTGCATTTAAGCATGTGCTACGTCATCCTATAATAGAAAATGGgtagggctgt ... taacttgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGAGTGTGACCATCTTGTGCATGAGGGGTTTGAAAGCACTGTAAGTTTACTTTGCCCTGCCAACCACATCGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcttgtgcagatgcatgaagggtcctcttgtaatatttctctttaacttgcagGAGGCTAAAGAAGAAGCATTGGGTGATAGAGTGTGACCATCTTGTGCATGAGGGGTTTGAAAGCACTGTAAGTTTACTTTGCCCTGCCAACCACATCGGT
                                          ctttaac  putative branch site (score: 9)
                                     tttctctttaactt  CT-rich tract
                                taatatttctctttaa  TA-rich tract