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

gtatgtgaactagcaagttgttttagccattgctcccatgaagtttatgtttgtttgtaccacttgcttgttaacacattttttctgttgatatgcagATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGATATCTACCAGGATAAAATTTTGTTTTAGATAGCTGTATAGGCAACAACT

Basic information

species Oryza sativa
transcript LOC_Os05g50980.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g50980.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G807767_T03 (Zea mays), 3'ss of exon 11
--------------------gtatg-tgaactagcaagttgttt-----ta-----gccattgctcccatgaagtttatgtttg--tttgtaccacttgcttgttaa--cacattttttctgttgatatgcagATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGATATCTACCAGGATAAAATTTTGTTTTAGATAGCTGTATAGGCAACAACT-
                     |||| ||  ||||  | |  |||     ||     |   || |||       | || ||  |   ||| |   | | | ||||| |   || || ||||  |  ||  |||| ||||| || ||||||||| ||||||| ||||||||||| || ||| |||| || || ||||||| |||| |||| ||| | |  |    |||   | || 
gtaggtgaactacctatttgttatgatgggctagtgattgatttgtgtgtatatatgtttttactctgggactgcttgtggataattttttgaaagtaggttgttgagttaccttctttcattctatgcgcagGTATCGTCTGCACCGGAAGATGCTCCTACAGAAAATCATGGACGCACTGGACATATATCAGGATAGAATTCTGTTCTAGCT-GTAGAGGCGGCGCTACCTG
















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|454496|gb|D28219.1|D28219
EST:     AGATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAA                         ATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA
genomic: AGATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAAgtatgtgaac ... tgatatgcagATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA
EST: gi|38481283|gb|CF965372.1|CF965372
EST:     AGATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAA                         ATATCGGCTACACCGGAAGCTGCTCCTGCAGAAGATCATCGATGCATTGGA
genomic: AGATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAAgtatgtgaac ... tgatatgcagATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA
EST: gi|86890247|gb|CI321424.1|CI321424
EST:     ATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAA                         ATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA
genomic: ATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAAgtatgtgaac ... tgatatgcagATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA
EST: gi|86868384|gb|CI334172.1|CI334172
EST:     ATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAA                         ATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA
genomic: ATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAAgtatgtgaac ... tgatatgcagATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA
EST: gi|88978149|gb|CI384631.1|CI384631
EST:     ATTCTAGATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAA                         ATATCGGCTACACCGGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGG
genomic: ATTCTAGATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAAgtatgtgaac ... tgatatgcagATATCGGCTACACC-GGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGG
EST: gi|38470611|gb|CF954742.1|CF954742
EST:     ATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAA                         ATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA
genomic: ATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAAgtatgtgaac ... tgatatgcagATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA
EST: gi|88223679|gb|CI223528.1|CI223528
EST:     ATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAA                         ATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA
genomic: ATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAAgtatgtgaac ... tgatatgcagATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA
EST: gi|86504726|gb|CI147359.1|CI147359
EST:     ATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAA                         ATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA
genomic: ATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAAgtatgtgaac ... tgatatgcagATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGA

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: 43 (upstream exon), 50 (downstream exon)
Score: 7

ATTCTGATGGACATATCAGAAGAACACGTGAAATCGCAATCAAgtatgtgaac ... tgatatgcagATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGATATCTACCAGGATAAAATTTTGTTTTAGATAGCTGTATAGGCAACAACT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgtttgtttgtaccacttgcttgttaacacattttttctgttgatatgcagATATCGGCTACACCGGAAGCTGCTCCTGCAGAAAATCATCGATGCATTGGATATCTACCAGGATAAAATTTTGTTTTAGATAGCTGTATAGGCAACAACT
                                   ttttttctgtt  CT-rich tract
                           ttaacacatttttt  TA-rich tract