Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttgtttccatttttttatatttgtagtaactgccatagaccatgtatccaagatatgttactgtatcccctttcagGTTTGTTCTTGGGGAGGCTACACATTCATCATCAATCTTATCCCAATGCATGTTCTCTTGTGTATTGTGACTGGTCGTTACTCTTCACGACTTTATATTG

Basic information

species Zea mays
transcript GRMZM2G154165_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154165_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA16G08410.1 (Glycine max), 3'ss of exon 8
gtatttttgtttccatttttttatatttgtagtaactgccatagaccatg--tatccaagatatgttactgtatcccctttcagGTTTGTTCTTGGGGAGGCTACACATTCATCATCAATCTTATCCCAATGCATGTTCTCTTGTGTATTGTGACTGGTCGTTACTCTTCACGACTTTATATTG
|||   || | |     | ||||| || ||  |   |||    | ||     |||  | | ||| ||    | |   |||||||||||| || |||||||| ||||| || ||||| |||||||| |||||||||||||||||||| || || |||||||| || ||||| ||||| || ||||
gtaagcttttataatactatttatcttggttatctttgcttctgccccctcttatgtatgttatcttcgcttcttatctttcagGTTTGCTCATGGGGAGGGTACACTTTTATCATTAATCTTATTCCAATGCATGTTCTCTTGTGCATAGTAACTGGTCGCTATTCTTCTCGACTGTACATTG

upper sequence: GRMZM2G154165_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 8
----gtatttttgtttccattttt-----ttatatttgtagtaactgccatagaccatgtatccaagatatgttactgtatcccctttcagGTTTGTTCTTGGGGAGGCTACACATTCATCATCAATCTTATCCCAATGCATGTTCTCTTGTGTATTGTGACTGGTCGTTACTCTTCACGACTTTATATTG
    |  ||| |  | | |||| |     |||| ||||         ||    |   | | |  | | ||| ||    | |   |||||||||||| || |||||||| ||||| || ||||| |||||||| || |||||||| |||||||| || || || ||||| || ||||| ||||| || ||||
gtaagcttttataatactatttatcttggttatctttgcctctgtcccctcttatt-tatgtttatgttatcttcgcttcttatctttcagGTTTGCTCATGGGGAGGGTACACTTTTATCATTAATCTTATTCCGATGCATGTACTCTTGTGCATAGTAACCGGTCGCTATTCTTCTCGACTGTACATTG

upper sequence: GRMZM2G154165_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 8
gtatttttgttt-ccatttttttatat-ttgtagtaactgccatagaccatgtatccaagatatgttactgtatcccctttcagGTTTGTTCTTGGGGAGGCTACACATTCATCATCAATCTTATCCCAATGCATGTTCTCTTGTGTATTGTGACTGGTCGTTACTCTTCACGACTTTATATTG
|||   |||| | ||||| ||  |  | || |     |  |  ||     | |||           || | | |||  ||||||||||| ||||||||||| ||||| || || ||||| ||||| ||||||||||| ||  | || || || |||||||| || ||||| |||||||| ||||
gtagggttgtgtgccattgttgcaagtctttttactccccctttatggtgtttatgtttttgggtgtattatttcctttttcagGTTTGCTCTTGGGGAGGATACACTTTTATTATCAACCTTATTCCAATGCATGTGCTTCTTTGCATAGTAACTGGTCGCTATTCTTCTCGACTTTACATTG

upper sequence: GRMZM2G154165_T02 (Zea mays), 3'ss of exon 8
lower sequence: EFJ15189 (Selaginella moellendorffii), 3'ss of exon 8
gtatttttgtttccatttttttatatttgtagtaactgccatagaccatgtatccaagatatgttactgtatcccctttcagGTTTGTTCTTGGGGAGGCTACACATTCATCATCAATCTTATCCCAATGCATGTTCTCTTGTGTATTGTGACTGGTCGTTACTCTTCACGACTTTATATTG
                            ||| |   |   || |   ||  |||  |    |    || |   | | ||||||||||||| |||||||| || || || ||||||||| | || || |||||||| ||| | ||||||||||||||  | ||||| |||||  | ||||| |
----------------------------gtactcttttgtat-gtttataaatctga----ttcagctttgctctcgttcagGTTTGTTCCTGGGGAGGTTATACGTTTATCATCAATTTGATTCCGATGCATGTCCTCCTATGTATTGTGACTGGGAGATACTCATCACGGTTGTATATAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|76017470|gb|DT944640.1|DT944640
EST:     CTGGATCACTCTTTTATGCGGCACTTATTTCTCTCTCGTACTTCTACATG                         GTTTGTTCTTGGGGAGGCTACACATTCATCATCAATCTTATCCCAATGCAT
genomic: CTGGATCACTCTTTTATGCGGCACTTAATTCTCTCTCGTACTTCTACATGgtatttttgt ... cccctttcagGTTTGTTCTTGGGGAGGCTACACATTCATCATCAATCTTATCCCAATGCAT




















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: 110

ACACTAAACACTGGATCACTCTTTTATGCGGCACTTAATTCTCTCTCGTACTTCTACATGgtatttttgt ... cccctttcagGTTTGTTCTTGGGGAGGCTACACATTCATCATCAATCTTATCCCAATGCATGTTCTCTTGTGTATTGTGACTGGTCGTTACTCTTCACGACTTTATATTG


Block sizes: 42 (upstream exon), 30 (downstream exon)
Score: 13

ACACTAAACACTGGATCACTCTTTTATGCGGCACTTAATTCTCTCTCGTACTTCTACATGgtatttttgt ... cccctttcagGTTTGTTCTTGGGGAGGCTACACATTCATCATCAATCTTATCCCAATGCATGTTCTCTTGTGTATTGTGACTGGTCGTTACTCTTCACGACTTTATATTG


Block sizes: 39 (upstream exon), 30 (downstream exon)
Score: 8

ACACTAAACACTGGATCACTCTTTTATGCGGCACTTAATTCTCTCTCGTACTTCTACATGgtatttttgt ... cccctttcagGTTTGTTCTTGGGGAGGCTACACATTCATCATCAATCTTATCCCAATGCATGTTCTCTTGTGTATTGTGACTGGTCGTTACTCTTCACGACTTTATATTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 47

ACACTAAACACTGGATCACTCTTTTATGCGGCACTTAATTCTCTCTCGTACTTCTACATGgtatttttgt ... cccctttcagGTTTGTTCTTGGGGAGGCTACACATTCATCATCAATCTTATCCCAATGCATGTTCTCTTGTGTATTGTGACTGGTCGTTACTCTTCACGACTTTATATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagtaactgccatagaccatgtatccaagatatgttactgtatcccctttcagGTTTGTTCTTGGGGAGGCTACACATTCATCATCAATCTTATCCCAATGCATGTTCTCTTGTGTATTGTGACTGGTCGTTACTCTTCACGACTTTATATTG
  tagtaac  putative branch site (score: 47)
                                       ctgtatcccctttc  putative PPT
                               atatgtta  TA-rich tract