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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgagaaatcttccacttattgctgaaccatattttttggttgtgtttatggtctaagttacctgtacacagATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAG

Basic information

species Oryza sativa
transcript LOC_Os07g30980.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g30980.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G121427_T01 (Zea mays), 3'ss of exon 9
gttgagaaatcttccacttattgctgaaccatattttttggttgtgtttatggtctaagttacctgtacacagATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAG
||||| ||| | |     |  |    ||   | | |||      || ||  |  |||| || |   | ||||||| ||||||||||| ||||| |  || ||||||||||| |||||||| ||||| ||||||||||||||||||||||||||||||
gttgaaaaaacgtta---tgctttcaaaaggtgtcttt-----atgcttgcgacctaattttctcttgcacagATAACTGGCAAAGCTTTCCAAGTCTCCTTCCGCAACAGGAAAATTCCCTTTAACATTCATGGTGTGGCTTTCTACAGGAAAAAG

upper sequence: LOC_Os07g30980.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA20G34060.1 (Glycine max), 3'ss of exon 11
--------------gttgagaaatcttc-----cacttattgctgaaccatattttttggttgtgtttatggtctaagttacctgtacacagATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAG
               || | || | |||     || |||   ||  | |  | |   || || |   ||    ||   || |||||   |||||  | || ||||| |||||   | | |||||  | || ||||| || ||||| ||||||||||||||||| ||||| ||||||
gtgatgtttcttgcttttataactgttcaaaagcaattacc-ctatatctgactgaatgatttttactacaccctttctt-cctgt-ttcagATATCAGGTAAAGCCTTCCAAATGGCTTTCCGTGATAGGAAAATACCATTTAACATTCATGGTGTGGCTTTTTACAGAAAAAAG

upper sequence: LOC_Os07g30980.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT4G25120.1 (Arabidopsis thaliana), 3'ss of exon 11
---------------------gttgagaaatcttc----cacttattgctgaaccatattttttggttgtgtttatggtctaagt---tacctgtacacagATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAG
                     | ||| |     |        |||    |  | |||||||  |  | |||||  |   | | |    |||   ||  ||| |  | || ||||  || ||     |||||||| | |||||||| || |||||  |||||||||| ||||||||||||||||||
gtcagtccttttcttttccttgatgacatgctgttagaatgtttaaaattttaacatatttacttat-gtgttggtaaaccatgaatgtactgatattcagGTGTCAGGTAAAGTGTTTCAAAATGCATTCCGCCAGAGAAAAATACCATTTAACGTTCATGGTGTTGCTTTCTACAGGAAAAAG

upper sequence: LOC_Os07g30980.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv16s0013g00300.t01 (Vitis vinifera), 3'ss of exon 10
----------------------gttgagaaatcttccacttattgc-tgaac-catat---tttttggttgtgtttatggtctaagttacctgtacacagATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAG
                       || | | |  |   | |  |||  ||||| || ||    | |||||   ||  ||| |  |  || | ||  ||||| |  |||| |||| ||||||  |  | || ||  | || || || || ||||| |||||||||||||| |||||||||||||||
gtcaagctatctgtatcataatcttaaaacacatgaaagtacttgtatgaacacacataaactattggtatggtgcatgctgaagctttcatgc-cacagGTATCTGGAAAAGTATTCCAAACAGCCTTTCGTGATAGGAAGATACCGTTTAACATTCATGGTGTGGCCTTCTACAGGAAAAAG

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|88509079|gb|CI436585.1|CI436585
EST:     CAGTTGAAGGATGTCATTTTGGCAAAATTGCTGTCCTATATCGCAGACAG                         ATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTT
genomic: CAGTTGAAGGATGTCATTTTGGCAAAATTGCTGTCCTATATCGCAGACAGgttgagaaat ... ctgtacacagATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTT
EST: gi|58662033|gb|CK050713.1|CK050713
EST:     CAGTTGAAGGATGTCATTTTGGCAAAATTGCTGTCCTATATCGCAGACAG                         ATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTT
genomic: CAGTTGAAGGATGTCATTTTGGCAAAATTGCTGTCCTATATCGCAGACAGgttgagaaat ... ctgtacacagATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTT
EST: gi|88592693|gb|CI710815.1|CI710815
EST:     TATCGCAGACAG                         ATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTT
genomic: TATCGCAGACAGgttgagaaat ... ctgtacacagATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTT
EST: gi|88371820|gb|CI680930.1|CI680930
EST:     TATCGCAGACAG                         ATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTT
genomic: TATCGCAGACAGgttgagaaat ... ctgtacacagATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTT

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: 51 (upstream exon), 48 (downstream exon)
Score: 11

TTCACAATGTGCATTTGTTATTGACAAGATTATTGAAACCACATCTAGTTCAGTTGAAGGATGTCATTTTGGCAAAATTGCTGTCCTATATCGCAGACAGgttgagaaat ... ctgtacacagATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgctgaaccatattttttggttgtgtttatggtctaagttacctgtacacagATCACTGGCAAAGCATTCCAGGCGTCATTCCGCAACAGAAAAATTCCTTTTAATATTCATGGTGTGGCTTTCTACAGGAAAAAG
            atatttttt  TA-rich tract