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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttttttcaagtatatatggatcaaacatgatattttttatgtttttcaactggaatttcacacagtaccatttttctatctgatagctagaagttttgtagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTCTCAGGAACAAATCAATTATTCTATCCTCAGACTTGGGCCTTTGCAGTAATTGTAG

Basic information

species Zea mays
transcript GRMZM2G104147_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104147_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 5
gtatgttttttttcaagtatatatggatcaaacatgat--attttttatgtttttcaactggaatttcacacagtaccatttttctatctgatagctagaagttttgtagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTCTCAGGAACAAATCAATTATTCTATCCTCAGACTTGGGCCTTTGCAGTAATTGTAG
||| | ||  | || |  |||||||   ||| ||| ||  ||||| |   |||||| ||||   |||||   |    |  | ||||||||||| |  |||| |||   |||| |||||||||| |||||| || ||||| |||||| ||||||||||||||   || || ||||||||||||||||| ||||| |||||  |||||||||
gtacgcttcctgtccaa-atatatgacccaatcataatcaattttgttgttttttctactgttgtttcaactaaattccatgttctatctgatggtgagaa-tttaacagGTGATGAGTGTAAAAGCTCTCGGCATTGCATTGAAGTTAACATTCTCAGGAGTGAACCAGTTATTCTATCCTCAGACATGGGCTTTTGCCCTAATTGTAG

upper sequence: GRMZM2G104147_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT1G71900.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgttttttttcaagtatatatggatcaaacatgatattttttatgtttttcaactggaatttcacacagtaccatttttct--atctgatagc-tagaagttttg--tagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTCTCAGGAACAAATCAATTATTCTATCCTCAGACTTGGGCCTTTGCAGTAATTGTAG
||||||  |||||   ||||       || |   ||  ||  ||||| | |||  |   |||| |       | ||| ||| |   |  |||||   |  || || ||   |||| |||||||||| ||| |||||||| || || ||||| || || |||||||||||||| ||||| |||||||| || |||   ||  |  |  | ||| 
gtatgtagttttt--ggtat------ttccagtttgtaatcctttatttctttaga--agaatgttg----attccactttgcctaaattgatattgtcaaacttgtgaacagGTAATGAGTGTAAAAGCACTTGGAATAGCATTAAAGCTGACCTTTTCAGGAACAAATCAGTTATTTTATCCTCAAACATGGATATTCACCTTGGTCGTAC
















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: 42 (upstream exon), 48 (downstream exon)
Score: 35

TGCGTCAGCCTTAGTGCTTATATATTTTGTTGTCCCTCATCATGGACAAACAAACATAATGGTGTACATTGGAGTTTGTTCTCTTCTAGGATCACTTACGgtatgttttt ... agttttgtagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTCTCAGGAACAAATCAATTATTCTATCCTCAGACTTGGGCCTTTGCAGTAATTGTAG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 36

TGCGTCAGCCTTAGTGCTTATATATTTTGTTGTCCCTCATCATGGACAAACAAACATAATGGTGTACATTGGAGTTTGTTCTCTTCTAGGATCACTTACGgtatgttttt ... agttttgtagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTCTCAGGAACAAATCAATTATTCTATCCTCAGACTTGGGCCTTTGCAGTAATTGTAG


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 24

TGCGTCAGCCTTAGTGCTTATATATTTTGTTGTCCCTCATCATGGACAAACAAACATAATGGTGTACATTGGAGTTTGTTCTCTTCTAGGATCACTTACGgtatgttttt ... agttttgtagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTCTCAGGAACAAATCAATTATTCTATCCTCAGACTTGGGCCTTTGCAGTAATTGTAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 48

TGCGTCAGCCTTAGTGCTTATATATTTTGTTGTCCCTCATCATGGACAAACAAACATAATGGTGTACATTGGAGTTTGTTCTCTTCTAGGATCACTTACGgtatgttttt ... agttttgtagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTCTCAGGAACAAATCAATTATTCTATCCTCAGACTTGGGCCTTTGCAGTAATTGTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactggaatttcacacagtaccatttttctatctgatagctagaagttttgtagGTTATGAGTGTAAGAGCTCTTGGAATTGCCTTGAAGCTAACATTCTCAGGAACAAATCAATTATTCTATCCTCAGACTTGGGCCTTTGCAGTAATTGTAG
                               atctgat  putative branch site (score: 48)
                       atttttctat  TA-rich tract