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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtatcatgagcttatatcacctcatttagccattagtataggttatcatccttgcctctgttccatgcagATTATCCATGTTAATCTTACTCAAGAAAGCCCAAAGCTTATTGATGTGAATAAGGCATTGGATATGACATATTCTGTCAAATGGGAACCAACAAACATAA

Basic information

species Zea mays
transcript GRMZM2G165631_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 5
gtttgtgtatcatgagcttatatcacctcattt---agccattagtataggttatcatccttgcctctgt-tccatgcagATTATCCATGTTAATCTTACTCAAGAAAGCCCAAAGCTTATTGATGTGAATAAGGCATTGGATATGACATATTCTGTCAAATGGGAACCAACAAACATAA
||||| || |||||| |||  ||    || ||     | | ||     |  | |  ||   | |   |   | | || ||||||| ||||||||||||||||||||||| |||||||||||||||| |  |||||||||||||||||||||||||||||| ||||||||||| ||  |||
gtttgggtttcatgaacttgcatttattccttcgcaggaccttcaagaaactgagtattactactgttacattcctgtagATTATTCATGTTAATCTTACTCAAGAAAGTCCAAAGCTTATTGATGCGGGTAAGGCATTGGATATGACATATTCTGTCAAGTGGGAACCAACCAATGTAA

upper sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 5
----------gtttgtgtatcatgagcttatatcacctcat-ttagccattagtataggttatcatccttgcctctgtt-ccatgcagATTATCCATGTTAATCTTACTCAAGAAAGCCCAAAGCTTATTGATGTGAATAAGGCATTGGATATGACATATTCTGTCAAATGGGAACCAACAAACATAA
           |||   |||| |  ||| || | |   ||  |||   | |  |  | ||| ||||  |    |||||| || |||||||||| ||||||||||| ||||| || | |||||||| | | || ||    ||    ||||| |||||||||||||||||||||||  | || ||  | |
gttagaagttatttaaatatcttatgct-atcttatgacaggttatggaatccttgaagtt-tcatattaaggtctgtttccttgcagATTATTCATGTTAATCTCACTCAGGATATCCCAAAGCCTTTGGAAGTAGGAAAACATTTGGACATGACATATTCTGTCAAATGGGATTCTACCAATGTCA
















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: 48 (upstream exon), 48 (downstream exon)
Score: 100

GTTTTGTTGGAGAGGCAGACAGAAACAATGATAACAAATATTTCCTATTCACGCACAAGAATATTGTCATCAGATACAATGGCAATCAGgtttgtgtat ... ttccatgcagATTATCCATGTTAATCTTACTCAAGAAAGCCCAAAGCTTATTGATGTGAATAAGGCATTGGATATGACATATTCTGTCAAATGGGAACCAACAAACATAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 90

GTTTTGTTGGAGAGGCAGACAGAAACAATGATAACAAATATTTCCTATTCACGCACAAGAATATTGTCATCAGATACAATGGCAATCAGgtttgtgtat ... ttccatgcagATTATCCATGTTAATCTTACTCAAGAAAGCCCAAAGCTTATTGATGTGAATAAGGCATTGGATATGACATATTCTGTCAAATGGGAACCAACAAACATAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 55

GTTTTGTTGGAGAGGCAGACAGAAACAATGATAACAAATATTTCCTATTCACGCACAAGAATATTGTCATCAGATACAATGGCAATCAGgtttgtgtat ... ttccatgcagATTATCCATGTTAATCTTACTCAAGAAAGCCCAAAGCTTATTGATGTGAATAAGGCATTGGATATGACATATTCTGTCAAATGGGAACCAACAAACATAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 127

GTTTTGTTGGAGAGGCAGACAGAAACAATGATAACAAATATTTCCTATTCACGCACAAGAATATTGTCATCAGATACAATGGCAATCAGgtttgtgtat ... ttccatgcagATTATCCATGTTAATCTTACTCAAGAAAGCCCAAAGCTTATTGATGTGAATAAGGCATTGGATATGACATATTCTGTCAAATGGGAACCAACAAACATAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacctcatttagccattagtataggttatcatccttgcctctgttccatgcagATTATCCATGTTAATCTTACTCAAGAAAGCCCAAAGCTTATTGATGTGAATAAGGCATTGGATATGACATATTCTGTCAAATGGGAACCAACAAACATAA
                                 tccttgcctctgttcc  CT-rich tract
                attagtata  TA-rich tract