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'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcaaacaacaccagattttttttttttgaaaatttgattgttttgaataccttttcttaaccattcttaaaccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTATTGGGGAGTCGCTACAGGGAAAGGACAACAACCGCCATCATATGGCATGG

Basic information

species Oryza sativa
transcript LOC_Os01g39380.2
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39380.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 2
gtgagtcaaacaacaccagattttttttttttgaaaatttgattgttttgaatacct--tttcttaaccattcttaaaccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTATTGGGGAGTCGCTACAGGGAAAGGACAACAACCGCCATCATATGGCATGG
|| ||||||||  || |     ||||    |||| |||| | ||| ||| || || |  |||||||    ||||  |  | || |||||||||||||||||||||||||||||||||||||||||| || |||||||||||||| || |||||||||||| | |||| |  ||  |||||||||||||
gtaagtcaaactgcaac-----ttttgacattgagaatt-ggttgctttaaacacttggtttcttacattttctctacacttcttcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTCCGGATTGGCTATTGGGGGGTTGCTACAGGGAAAAGCCAACCATTGCAGTCATATGGCATGG
















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|58659341|gb|CK048021.1|CK048021
EST:     ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
EST: gi|701649|gb|D47940.1|D47940
EST:     ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
EST: gi|87023608|gb|CI286359.1|CI286359
EST:     AGCTGAGAGAAACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: AGCTGAGAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
EST: gi|27576987|gb|CA999681.1|CA999681
EST:     GAGAAACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: GAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
EST: gi|3763545|gb|AU030297.1|AU030297
EST:     AACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: AACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
EST: gi|163918523|gb|EG713217.1|EG713217
EST:     ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
EST: gi|163926766|gb|EG715054.1|EG715054
EST:     ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT

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: 70 (upstream exon), 48 (downstream exon)
Score: 9

GCTGGACTGGGACTATCTGATATTGATTCTTGGAATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTATTGGGGAGTCGCTACAGGGAAAGGACAACAACCGCCATCATATGGCATGG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaatttgattgttttgaataccttttcttaaccattcttaaaccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTATTGGGGAGTCGCTACAGGGAAAGGACAACAACCGCCATCATATGGCATGG
                            tcttaac  putative branch site (score: 9)
                                             ccctcctc  putative PPT
              ttttgaata  TA-rich tract