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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATTACGGCTGAGGATAGAGGATCCTCCTCGGAGAAAGCACATGGTGTATCTGGGAGGTGCAGTGCTTGCTGGGATCATGAAGgtaattcttgtatatgcgaatggcatttacactgtgatggattgctagcaatatacttccccgcgtactgtttggaacgtgcag

Basic information

species Zea mays
transcript GRMZM2G342386_T02
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G342386_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os08g28190.1 (Oryza sativa), 5'ss of exon 14
AAATTACGGCTGAGGATAGAGGATCCTCCTCGGAGAAAGCACATGGTGTATCTGGGAGGTGCAGTGCTTGCTGGGATCATGAAGgtaattcttgtatatgcgaatggcatttacactgtgatggattgctagcaatatacttccccgc-gtactgtttggaacgtgcag-----------------------------------------------------------------------------------------------------
||||| ||  || ||||||||||||| || |||||||| |||||||| || ||||| |||||||| || ||||| ||||||||||||||     | |     |  |  || ||  || |     |||   |||||     |    |   |||  |    ||||    |                                                                                                      
AAATTGCGTTTGCGGATAGAGGATCCGCCACGGAGAAAACACATGGTTTACCTGGGTGGTGCAGTACTCGCTGGAATCATGAAGgtaatatacttttcccacagcgttatatat-ctatcggttattataagcaaagccttgggacaaagtagagaggtgaacagaaaaggagcacaaaagatgaaatcatgcattactgtgtgtgcattgtcgcatgggaatctgctcattttgctttattactttgctgacggctgttcacctagcag

upper sequence: GRMZM2G342386_T02 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA16G05780.1 (Glycine max), 5'ss of exon 14
AAATTACGGCTGAGGATAGAGGATCCTCCTCGGAGAAAGCACATGGTGTATCTGGGAGGTGCAGTGCTTGCTGGGATCATGAAGgtaattcttgtatat--gcgaatggcatttacactgtg-atggattg--ctagcaatatacttcc-----ccgcgtactgtttggaacgtgcag
|||||||| || || || |||||||| || || || |||||||||||||| || |||||||| || ||||| || || |||||||||    ||   | |    |  | |  ||| | ||  | || |  |   ||  |||| ||  |       |     ||   ||  ||    |||
AAATTACGACTAAGAATTGAGGATCCACCACGTAGGAAGCACATGGTGTACCTTGGAGGTGCTGTCCTTGCAGGAATAATGAAGgtatgagttagttgttaatgttttggtttttctctaggcataggcttatctgtcaatgtagatgtgaaagctattgacatattttaaaactcag

upper sequence: GRMZM2G342386_T02 (Zea mays), 5'ss of exon 14
lower sequence: Vv14s0068g01630.t01 (Vitis vinifera), 5'ss of exon 14
AAATTACGGCTGAGGATAGAGGATCCTCCTCGGAGAAAGCACATGGTGTATCTGGGAGGTGCAGTGCTTGCTGGGATCATGAAGgtaattcttgtata------tgcgaatggcatttacactgtg------------atggatt---gcta-gcaatatacttccccgcgtactgtttggaacgtgcag---------------------------------------------------------------------
||| | ||  || ||||||||||||| || || |||||||| |||||||| || ||||||||||| ||||| || || ||||||||   | |||   |      | |   | | ||||   ||               |||| ||   |||   | | ||  |  |   | | || |   |   |  |||                                                                     
AAACTGCGATTGCGGATAGAGGATCCACCACGAAGAAAGCATATGGTGTACCTTGGAGGTGCAGTCCTTGCAGGAATTATGAAGgtgccttttgctcaaacctttactgcttgtatttctgctccataatttaactgaatgggtttatgctgtactaaatcttctcttccctgctttcaagtctggccagcagaaaaccgaccttttgatgttttaattgcttgatcatttatttgattttgctggtgaaccaatgtag

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), 48 (downstream exon)
Score: 396

AAATTACGGCTGAGGATAGAGGATCCTCCTCGGAGAAAGCACATGGTGTATCTGGGAGGTGCAGTGCTTGCTGGGATCATGAAGgtaattcttg ... gaacgtgcagGATGCACCTGAGTTCTGGATAACCAGGCAGGAGTACCAGGAAGAAGGTGTAGCGTGCCTAAGGAAGTGCGGGCAGTCATAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 204

AAATTACGGCTGAGGATAGAGGATCCTCCTCGGAGAAAGCACATGGTGTATCTGGGAGGTGCAGTGCTTGCTGGGATCATGAAGgtaattcttg ... gaacgtgcagGATGCACCTGAGTTCTGGATAACCAGGCAGGAGTACCAGGAAGAAGGTGTAGCGTGCCTAAGGAAGTGCGGGCAGTCATAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 121

AAATTACGGCTGAGGATAGAGGATCCTCCTCGGAGAAAGCACATGGTGTATCTGGGAGGTGCAGTGCTTGCTGGGATCATGAAGgtaattcttg ... gaacgtgcagGATGCACCTGAGTTCTGGATAACCAGGCAGGAGTACCAGGAAGAAGGTGTAGCGTGCCTAAGGAAGTGCGGGCAGTCATAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 322

AAATTACGGCTGAGGATAGAGGATCCTCCTCGGAGAAAGCACATGGTGTATCTGGGAGGTGCAGTGCTTGCTGGGATCATGAAGgtaattcttg ... gaacgtgcagGATGCACCTGAGTTCTGGATAACCAGGCAGGAGTACCAGGAAGAAGGTGTAGCGTGCCTAAGGAAGTGCGGGCAGTCATAA