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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttcataccttttctgcatagataacatcttgaatgccatgcacctccagaattctgataaaaaaatgataattacacagGTCATTGAAACTAATAGGGCTGAAGAGTCACAAGGTCATGTACACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA

Basic information

species Zea mays
transcript GRMZM2G412234_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412234_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g09246.1 (Oryza sativa), 3'ss of exon 14
gtacttcataccttttctgcatagataacatcttgaatgccatgc-acctcca-gaattctgataaaaaaatga--taattac-acagGTCATTGAAACTAATAGGGCTGAAGAGTCACAAGGTCATGTACACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA
||| || ||||      | | |      ||| |||  ||||||   |||  || |  |||| ||| ||   |    |  ||    |||||| | ||||||||||||||||| || || || || |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
gtattttatacaccgcttccgt------catgttgtgtgccatatgaccatcatgggttctcatagaagttttttttgtttgttgcagGTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATGTATTTCATGGGCCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA

upper sequence: GRMZM2G412234_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G03550.1 (Glycine max), 3'ss of exon 16
------------gtacttcataccttttctgcatagataacatcttgaatgccatgcacctccagaattctgataaaaaaatgataattacacagGTCATTGAAACTAATAGGGCTGAAGAGTCACAAGGTCATGTACACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA
             | | |  |   |||   | |||   |  | |||   ||  |||   |     ||||    |   ||  |  | |     ||| | || ||||| || ||   ||| || || |   ||||||| |||||| ||||||||  ||| || || || |||||||||||||||||||| || ||  
gtccataactaacttccttgtgaatttcagggatactcattacctt---tggaatgttaccatcaaatttaactttgaattttgtgagctttcagATTATGGAAACAAACAGAAGTGAGGAATCTCCGAGTCATGTGCACAGGTTGTATTTCCAGGGCCCAAATACATTCAGTGAACCTTGGCATCTACCTCATT

upper sequence: GRMZM2G412234_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 14
----------gtacttcataccttttctgcatagataacatcttgaatgccatgcacctc-cagaatt------ctgataaaaaaatgataattacacagGTCATTGAAACTAATAGGGCTGAAGAGTCACAAGGTCATGTACACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA
          || |   | || |  |      | ||||       ||  |     |  |  |||  ||      ||| | | ||  | ||  ||   |||||  | ||||| ||||| |||||  | || ||  ||||||| || || |||||||| |||||||| || || ||||||||||| ||||||||| ||||||
agtaatgtttgttcaaaagacataattcagcgaaataatccgccaaacactccttatattacagtgttgtgctgctgtttataatgttattctttgtcagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATGTATTTTATGGGTCCTAATACATTCAGTGAACCGTGGCATCTCTCACACA

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), 49 (downstream exon)
Score: 63

TATGAAGTTTGTTGGCACTGATGAGTTACCTGGGCCGGCACCAACTCATCAAGGGTCCCAAATTGATCATTCCTTTCCCTTCCTAGAATCACTAAATGAGgtacttcata ... aattacacagGTCATTGAAACTAATAGGGCTGAAGAGTCACAAGGTCATGTACACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 93

TATGAAGTTTGTTGGCACTGATGAGTTACCTGGGCCGGCACCAACTCATCAAGGGTCCCAAATTGATCATTCCTTTCCCTTCCTAGAATCACTAAATGAGgtacttcata ... aattacacagGTCATTGAAACTAATAGGGCTGAAGAGTCACAAGGTCATGTACACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 105

TATGAAGTTTGTTGGCACTGATGAGTTACCTGGGCCGGCACCAACTCATCAAGGGTCCCAAATTGATCATTCCTTTCCCTTCCTAGAATCACTAAATGAGgtacttcata ... aattacacagGTCATTGAAACTAATAGGGCTGAAGAGTCACAAGGTCATGTACACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

TATGAAGTTTGTTGGCACTGATGAGTTACCTGGGCCGGCACCAACTCATCAAGGGTCCCAAATTGATCATTCCTTTCCCTTCCTAGAATCACTAAATGAGgtacttcata ... aattacacagGTCATTGAAACTAATAGGGCTGAAGAGTCACAAGGTCATGTACACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcttgaatgccatgcacctccagaattctgataaaaaaatgataattacacagGTCATTGAAACTAATAGGGCTGAAGAGTCACAAGGTCATGTACACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA
                           ttctgat  putative branch site (score: 158)
                       agaattctgataaaaa  TA-rich tract