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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctttggacagactgcagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcag

Basic information

species Oryza sativa
transcript LOC_Os12g03720.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03720.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G005849_T01 (Zea mays), 5'ss of exon 9
GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctttggacagactgcagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcag
|||| |||||||| ||||| || |||||||| || || || || || ||||| || ||||| || ||||| |||||||| || || || |||||||||||||||      |  | |  |    |  ||  ||   || |  ||  |  |   ||||   |  |      ||   |||||||||||
GCGAGGGCATGCTCGCTGGCGAGATGAAGCACGGGCCGCTGGCCCTCGTGGACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaa---tgataaagaagcatgggcccagctttggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcag

upper sequence: LOC_Os12g03720.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA09G38460.1 (Glycine max), 5'ss of exon 9
GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctttggacagactgcagagcacgttcattttcttttcatttttcaaggagttcctctaaacat-cttcacctcttgcag
| ||||| |||||||||||||||||||||||||| ||  | ||| ||||||||||||| || || ||    ||  | ||||| |||||||| ||||||||||  |   |       |||||  ||| |  || ||| |||         | | |   ||  | |  ||||  || | || |  |||
GTGAAGGGATGCTTGCTGGTGAAATGAAGCATGGTCCTTTGGCATTAGTGGATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgt-------gactgtcgagtagctttattatctgaaa-----ttaggagtttgatattgacatattttatctttgacag

upper sequence: LOC_Os12g03720.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv13s0064g00050.t01 (Vitis vinifera), 5'ss of exon 9
GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagc-gctttggacag----actgcagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttc-acctcttgcag
| ||||| ||  |||| ||||||||||| ||||| ||  | || ||||| |||||||| ||||| ||  | || |||||||| |||||||| |||||||||| ||    |||  |       | || |   |    | | ||  ||  |||| |||  |   ||  | |  |||| ||| |   ||  |||
GTGAAGGAATAATTGCAGGTGAAATGAAACATGGTCCTTTGGCTCTAGTTGATGAAAATCTTCCAATTGTTGTTATTGCTACCCGTGATGCTTGCTTCAGgttagttattttttatttttttattgaaagacttaataagttgtttgacattcttcttgc--tttgtattgacattttctaatgctgacag

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|86426649|gb|CI071746.1|CI071746
EST:     GATGAAAACCTTCCGATGATCGTCATTGCTACACGTGATGCGTGCCTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|88902738|gb|CI088276.1|CI088276
EST:     TACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: TACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|58600045|gb|CK010573.1|CK010573
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|86479812|gb|CI122445.1|CI122445
EST:     GATGAAAACCTTCGGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|89184705|gb|CI007130.1|CI007130
EST:     GATG-AAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|87026077|gb|CI250093.1|CI250093
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|86834864|gb|CI345948.1|CI345948
EST:     ACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: ACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|88837681|gb|CI079041.1|CI079041
EST:     GCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|3766919|gb|AU031029.1|AU031029
EST:     GATGAAAA-CTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|86496093|gb|CI138726.1|CI138726
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|86481498|gb|CI124131.1|CI124131
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|88902955|gb|CI088493.1|CI088493
EST:     CTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: CTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT

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: 57 (upstream exon), 69 (downstream exon)
Score: 7

GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCAGTTTGCCCTAGTGGATCT




<











<


<