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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttaatgaagtttaaatgttgttctttgcgctatataaaatgctgagcaatctgttccaaagcagGACCCTGGAGAGGCAAACGTTGCAGCAGATCTTGACTCTAAGTTGGTAGTGTAAATATAAAGGTACCATTTCATGAATCATGATCAGGCACTTTATATGC

Basic information

species Zea mays
transcript GRMZM2G085970_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085970_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g06450.2 (Oryza sativa), 3'ss of exon 10
gtaagt-ttaatgaagtttaaatgt---tgttctttgcgctatataaaatgctgagcaatctgttccaaagcagGACCCTGGAGAGGCAAACGTTGCAGCAGATCTTGACTCTAAGTTGGTAGTGTAAATATAAAGGTACCATTTCA----TGAATCATGATCAGGCACTTTATATGC
||| || ||       ||| | | |   |||| ||| |  ||| | |||||||||||||||||||  |||  ||||  ||||||||||||||||||| || |  ||||| || ||||| || |||||||||| |||||| |   |        | || ||||   ||    | |    
gtacgtctttgctccatttcagtatatttgttatttactttatgtgaaatgctgagcaatctgttggaaaatagGATGCTGGAGAGGCAAACGTTGCGGCCGCACTTGATTCGAAGTTAGTGGTGTAAATATGAAGGTAACGCATTGGACTCCATTCCTGATATAGCTTGCTGT----

upper sequence: GRMZM2G085970_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g06450.1 (Oryza sativa), 3'ss of exon 10
gtaagt-ttaatgaagtttaaatgt---tgttctttgcgctatataaaatgctgagcaatctgttccaaagcagGACCCTGGAGAGGCAAACGTTGCAGCAGATCTTGACTCTAAGTTGGTAGTGTAAATATAAAGGTACCATTTCATGAATCATGATCAGGCACTTTATATGC
||| || ||       ||| | | |   |||| ||| |  ||| | |||||||||||||||||||  |||  ||||  ||||||||||||||||||| || |  ||||| || ||||| || |||||||||| |||                                      
gtacgtctttgctccatttcagtatatttgttatttactttatgtgaaatgctgagcaatctgttggaaaatagGATGCTGGAGAGGCAAACGTTGCGGCCGCACTTGATTCGAAGTTAGTGGTGTAAATATGAAG--------------------------------------
















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: 40 (upstream exon), 42 (downstream exon)
Score: 24

TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaa ... tccaaagcagGACCCTGGAGAGGCAAACGTTGCAGCAGATCTTGACTCTAAGTTGGTAGTGTAAATATAAAGGTACCATTTCATGAATCATGATCAGGCACTTTATATGC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 16

TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaa ... tccaaagcagGACCCTGGAGAGGCAAACGTTGCAGCAGATCTTGACTCTAAGTTGGTAGTGTAAATATAAAGGTACCATTTCATGAATCATGATCAGGCACTTTATATGC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 14

TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaa ... tccaaagcagGACCCTGGAGAGGCAAACGTTGCAGCAGATCTTGACTCTAAGTTGGTAGTGTAAATATAAAGGTACCATTTCATGAATCATGATCAGGCACTTTATATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 30

TGATCTCTCTGAATTTGATGAATCTCGAGAGATAATAGAGAGCCTAGTTGATGAATACAAGGCCTGTGAGTCGCCAGACTACATTAAATGGGGAATGGAGgtaagtttaa ... tccaaagcagGACCCTGGAGAGGCAAACGTTGCAGCAGATCTTGACTCTAAGTTGGTAGTGTAAATATAAAGGTACCATTTCATGAATCATGATCAGGCACTTTATATGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaatgttgttctttgcgctatataaaatgctgagcaatctgttccaaagcagGACCCTGGAGAGGCAAACGTTGCAGCAGATCTTGACTCTAAGTTGGTAGTGTAAATATAAAGGTACCATTTCATGAATCATGATCAGGCACTTTATATGC
                                        tctgttcc  CT-rich tract
                     tatataaaat  TA-rich tract