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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgccttgctcacccttatccattcctaccaccccatcacagaaaacttgtgtcgctgtgtacgattagtctaattaataataacaattaatctaaccaattgtgatctgaagatgctaacgtatgcgcatacattcatgcagTGGCGACGCCCAAGCAGATACGGGAGCTCATGAATGTCGACGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG

Basic information

species Zea mays
transcript GRMZM2G159119_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159119_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g22020.1 (Oryza sativa), 3'ss of exon 3
gtttgttgccttgctcacccttatccattcctaccaccccatcacagaaaacttgtgtcgctgtgtacgattagtctaattaataataacaattaatctaaccaattgtgatctgaagatgctaacgtatgcg-catacattcatgcagTGGCGACGCCCAAGCAGATACGGGAGCTCATGAATGTCGACGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
          ||  |  |  || | |      ||  | | | |  | ||| |   |  |  | |       ||    ||  || | ||   ||||||||  |   |  |  |    |  | | | |  ||  | |      | ||||||| ||||||||||||||||| |||||||| ||||| || || ||||||||||||||||||||||||||||||||||||
---------gttagtgccattttttctcagtgacagctcgaccggacaaaccaaattacattatcc-----tatatcaacaaacagtactgattaatctcgcttgtactagtt---aattacgagctaattagtcccgtgcttatgcagTAGCGACGCCCAAGCAGATCCGGGAGCTGATGAAGGTGGATGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG

upper sequence: GRMZM2G159119_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S83_100V6.1 (Physcomitrella patens), 3'ss of exon 4
gtttgttgccttgctcacccttatccattcctaccaccccatcacagaaaacttgtgtcgctgtgtacgattagtctaattaataataacaattaatctaaccaattgtgatctgaagatgctaacgtatgcgcatacattcatgcagTGGCGACGCCCAAGCAGATACGGGAGCTCATGAATGTCGACGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
                                    | |  |  | | |  ||  |  |  | ||| |   | ||    || ||  |       ||  | || ||||   |  |       || ||    ||   |    |  |||||| || ||||| ||||| ||||| ||||| ||||| ||||||||||| ||||||||||| || ||||||||| |||||
---------------------------------tttctctgtgtcggcattctccttgcattttgttc---tggt---gtttatgttggattcgaacttcacaaatt-caactt-----cactgacacgggc---tgtggttgtgcagTTGCCACGCCAAAGCAAATACGCGAGCTGATGAAGGTCGACGGCCTTACCAACGACGAAGTGAAGAGCCATCTGCAG

upper sequence: GRMZM2G159119_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ33402 (Selaginella moellendorffii), 3'ss of exon 3
gtttgttgccttgctcacccttatccattcctaccaccccatcacagaaaacttgtgtcgctgtgtacgattagtctaattaataataacaattaatctaaccaattgtgatctgaagatgctaacgtatgcgcatacattcatg-cagTGGCGACGCCCAAGCAGATACGGGAGCTCATGAATGTCGACGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
                                                                                   ||| |||  ||   ||      |     |||||      | ||     ||  |   ||  || |||| || ||||| ||||||||| | ||| ||||||| || || || ||||| |||||||| |||||||||||| | |||
----------------------------------------------------------------------------------gtaa-aacgtttttccttcttgctcaatctctga------tgacaagctcg-gtttgttggtgacagTCGCTACGCCTAAGCAGATAAGAGAGATCATGAAAGTAGATGGACTCACGAACGACGAAGTCAAGAGCCATCTTCAG

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 1 RNA-Seqlibrary.


Block sizes: 41 (upstream exon), 9 (downstream exon)
Score: 3

TCGCAGTCGCAGGCGCCCAGCCGGAAGGCGCGGCGGTGCTGGGCCCCGGAGCTCCACCGCCGGTTCCTACAGGCGCTGCAGCAGCTCGGCGGGTCCCACGgtttgttgcc ... attcatgcagTGGCGACGCCCAAGCAGATACGGGAGCTCATGAATGTCGACGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatctaaccaattgtgatctgaagatgctaacgtatgcgcatacattcatgcagTGGCGACGCCCAAGCAGATACGGGAGCTCATGAATGTCGACGGCCTCACCAACGACGAGGTCAAGAGCCATTTGCAG
                          tgctaac  putative branch site (score: 3)
                                         atacatt  TA-rich tract