Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCCTCCGCGTCCCCGGGGACACCTCCACCGCCTTCTCCGTCTTCGCGgtatccttcctcttccttgatctactactccattttattcattcattcattcactactcctcctcatcatgtcacgcgctggatccgtccgtctttgcttgcttgcttcgcctcag

Basic information

species Oryza sativa
transcript LOC_Os07g49040.1
intron # 1
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g49040.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G453296_T01 (Zea mays), 5'ss of exon 2
CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCCTCCGCGTCCCCGGGGACACCTCCACCGCCTTCTCCGTCTTCGCGgtatccttcctcttccttgatctactactccattttattcattcattcattcactactcctcctcatcatgtcacgcgctggatccgtccgtctttgcttgcttgcttcgcctcag
 |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| || |  |||| |||||||||||||| |||     |  | |||     |  |  |||  | |   ||   |   |   | || || | ||   |  || | |      | | |||   |||  ||  ||  |           
GCACGCCGGCTTCGCCAAGCGTGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCCTCCGCGTCCCCGGGGACCCCGCATCCGCGTTCTCCGTCTTCGCCgtacgtaccgccctccc--gcccgcctctctctctctctcg--cgcgcgcgcgctgctgcgccctgttctgacgcctctccgctgcgtggatcta-gcgcgccag-----------

upper sequence: LOC_Os07g49040.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G113016_T01 (Zea mays), 5'ss of exon 1
CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCCTCCGCGTCCCCGGGGACACCTCCACCGCCTTCTCCGTCTTCGCGgtatccttcctcttccttgatctactactccattttattcattcattcattcactactcctcctcatcatgtcacgcgctggatccgtccgt--ctttgcttgcttgcttcgcctcag
||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| || |  | || ||||| || ||||| |||     |  |  ||     ||    ||||| |       | | |||        |||   |||    ||    || ||| ||| | |  |  |||||||||  |    |||  |||
CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCGTCCGCGTCCCCGGGGACCCCGCATCGGCGTTCTCAGTTTTCGCCgtacgtaccgcccgcccctccctctctctccactgctaatgtcccttctcctctctctctctctctctctgctgtgccctg-atctgacgtttcctttgcttggatctggcgcggcag

upper sequence: LOC_Os07g49040.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G836628_T01 (Zea mays), 5'ss of exon 1
CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCCTCCGCGTCCCCGGGGACACCTCCACCGCCTTCTCCGTCTTCGCGgtat---ccttcctcttccttga-tctactactccattttattcattcattcattcactactcctc-ctcatcatgtcacgcgctggatccgtccgtcttt-gcttgcttgctt-cgcctcag--------------------------------------------
|||||||||||| |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| || |  |||| ||||||||||| || |||    ||  ||||   |  |  |||    |||  | |   ||  ||  ||  || ||    ||| |||    | || | | ||   ||  ||  ||| | ||  ||  ||   |||  | |                                            
CCACGCCGGCTTTGCCAAGCGTGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCCTCCGCGTCCCCGGGGACCCCGCATCCGCGTTCTCCGTCTTTGCCgtacgtaccgccctcccgcccgcctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctctcgcgcgcgcgcgcgcgctgctgcgccctgttctgacgcctctccgccgcgtggatctggcgcgcag

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|117246358|gb|CT843237.1|CT843237
EST:     ACTGCCTCCGCGTCCCCGGGGACACCTCCACCGCCTTCTCCGTCTTCGCG                         GTGTTCGACGGCCACAACGGGGTCTCGGCGGCGGTCTACAGCAAGGAGCAT
genomic: ACTGCCTCCGCGTCCCCGGGGACACCTCCACCGCCTTCTCCGTCTTCGCGgtatccttcc ... ttcgcctcagGTGTTCGACGGCCACAACGGGGTCTCGGCGGCGGTCTACAGCAAGGAGCAT
EST: gi|29671528|gb|CB667803.1|CB667803
EST:     ACTGCCTCCGCGTCCCCGGGGACACCTCCACCGCCTTCTCCGTCTTCGCG                         GTGTTCGACGGCCACAACGGGGTCTCGGCGGCGGTCTACAGCAAGGAGCAT
genomic: ACTGCCTCCGCGTCCCCGGGGACACCTCCACCGCCTTCTCCGTCTTCGCGgtatccttcc ... ttcgcctcagGTGTTCGACGGCCACAACGGGGTCTCGGCGGCGGTCTACAGCAAGGAGCAT

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 1 RNA-Seqlibrary.


Block sizes: 45 (upstream exon), 73 (downstream exon)
Score: 4

CCACGCCGGCTTCGCCAAGCGCGGCGAGGACTACTTCCTCGTCAAGCCCGACTGCCTCCGCGTCCCCGGGGACACCTCCACCGCCTTCTCCGTCTTCGCGgtatccttcc ... ttcgcctcagGTGTTCGACGGCCACAACGGGGTCTCGGCGGCGGTCTACAGCAAGGAGCATTTGCTCGAGCACGTCATGAGCGCGCTGCCGCCGGACATCGGCCGCGACG




<











<


<