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

ATTCTCCATCCAGGAGGGATGGCATTGATTTGAAGAAAGAGTCTTACCTCCGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcatagttgatttaacttatatttttcattgttgatgttaacttgttcctttcaatcattattatgatcttcaattaccatgatgcatgcattt...

Basic information

species Oryza sativa
transcript LOC_Os12g30020.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G115670_T01 (Zea mays), 5'ss of exon 1
ATTCTCCATCCAGGAGGGATGGCATTGATTTGAAGAAAGAGTCTTACCTCCGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcatag---ttgatttaacttatatttttcattgttgatgttaacttgttcctttcaatcattattatgatcttcaattaccatgatgcatgcattt
||||||||||||||||||||| |||||||||||||||||||| |  ||| ||||| || ||||| | ||||||||||||||||||||||| ||||||||||||||||   ||   ||||| ||  |  |   | || |   |     |   |   | ||   ||| ||  |||  ||       |||  | ||          
ATTCTCCATCCAGGAGGGATGACATTGATTTGAAGAAAGAGTGTAGCCTTCGAAAGTCGTATTGCAGTTTTCTACAAGATTTGGGCATGAAGCTTAAAGTgtaagattggagacattgatctacttgttggctatcttgcatttcactttttaaattctaggaatgatatttaaaatgaagtgctactttaatatccagg---

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G377311_T01 (Zea mays), 5'ss of exon 2
ATTCTCCATCCAGGAGGGATGGCATTGATTTGAAGAAAGAGTCTTACCTCCGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcatag--ttgatttaacttatatttttcattgttga-tgttaact-tgttcc--tttcaatcattattatgatcttcaattaccatgatgcatgcattt
| ||||||||||||||||||||||| ||||||||||||||||||  | | || || | |||||| |  ||||||||||| |||||||||  ||||||| ||||||||       || ||||  ||||| || |  |||||||  ||||   | ||||||  |||| |  | |  ||  | |   | |||  |||| |         
ACTCTCCATCCAGGAGGGATGGCATCGATTTGAAGAAAGAGTCTAGCATTCGGAAGTTATATTGCAAGTTTCTACAAGAGTTGGGCATGGCGCTTAAAATgtaagattgggacatttatttt-cttatcttatatattgttggctgttctttgtgttccactttctacaaattctaataacactatttaaaatgaagtgct-----

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA15G41040.1 (Glycine max), 5'ss of exon 1
ATTCTCCATCCAGGAGGGATGGCATTGATTTGAAGAAAGAGTCTTACCTCCGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcatagttgatttaacttatatttttcattgttgatgttaacttgttcctttcaatcattattatgatcttcaatta-ccatgatgcatgcattt-
| || |||||||     |||||||| ||||||||||||||  ||||||| || |||||||| ||||| ||||| ||||| || |||||||| |||||||||| || || |  ||| ||       |    |   ||        ||    | || ||| |  | || | ||    | |||||| || || | | |   | | 
ACTCACCATCCAAACACGATGGCATAGATTTGAAGAAAGAAACTTACCTACGCAAATCATACTGTACATTTCTGCAAGACTTAGGCATGAGACTTAAAGTgtgag-tctttattggttgcctcagtggcctatcttaactgcaataggagggtcttttgagac-ttgtgatttattgcaattatccttggttcctatttgtt

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G17960.1 (Glycine max), 5'ss of exon 1
ATTCTCCATCCAGGAGGGATGGCATTGATTTGAAGAAAGAGTCTTACCTCCGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcatagttgatttaacttatatttttcattgttgatgttaacttgttcctttcaatcattattatgatcttcaattaccatgatgcat-gcattt
| || |||||||     |||||||| ||||||||||||||  ||||||| || |||||||| ||||| ||||| ||||| || |||||||| |||||||||| || || |   || ||       |    |   ||        ||    |  | |||   |  | | | ||    | ||      ||||  || |||  |
ACTCACCATCCAAACACGATGGCATAGATTTGAAGAAAGAAACTTACCTACGCAAATCATACTGTACATTTCTGCAAGACTTAGGCATGAGACTTAAAGTgtgag-tctttactggttgcctcagtgacctatcttaactgcaatagggggcacttttgttttttaaatttgcctgttaagacttgtgatttattgcaagt

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv19s0027g01670.t01 (Vitis vinifera), 5'ss of exon 1
ATTCTCCATCCAGGAGGGATGGCATTGATTTGAAGAAAGAGTCTTACCTCCGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcatagttgatttaacttatatttttcattgttg-atgttaacttgttcctttcaatcattattatgatcttcaattaccatgatgcatgcattt-
|||| || |||| | | ||||| ||||||||||| |||||| ||||||| || || || || ||||| |||||||| ||||||||||||||||| ||||||||||     |  |  |  | |  ||  | |  ||||       ||  | |||| ||||   |   |   || |   ||| |    |  ||    | | || 
ATTCCCCTTCCAAGCGTGATGGAATTGATTTGAAAAAAGAGACTTACCTACGCAAGTCGTACTGTACATTTCTACAGGATTTGGGCATGAGGCTCAAAGTgtaagtcatgaacttgtcaagc--attgtctgaattgccatgcctttccctgtttctttggttacatgcaataactctcattgtttaccatttcagtacttt

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 5'ss of exon 1
ATTCTCCATCCAGGAGGGATGGCATTGATTTGAAGAAAGAGTCTTACCTCCGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatc-ata------gttgatttaacttatatttttcatt---gttgatgttaacttgttcctttcaatcattattatgatcttcaattaccatgatgcatgcattt
|||| ||||| || || ||||||||||| |||| ||||||| | ||  ||||||||||||| || |||||  | || ||||| ||||||||||||||||||||||  | |||      |||| | |   |||| | |    ||     || |  ||     ||| ||    | |||  |   |||    ||| |     |||||      
ATTCCCCATCAAGAAGAGATGGCATTGACTTGAGGAAAGAGACATATTTCCGAAAATCATACTGCACTTTCTTGCAGGATTTAGGCATGAGGCTTAAAGTgtaagtcctatacaaaatgttgttctggattatgtctcctttttgaactggttgtaggcaattctttcaggtaattggttgcatc----atttcaggtttgcat------

upper sequence: LOC_Os12g30020.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S119_132V6.1 (Physcomitrella patens), 5'ss of exon 1
ATTCTCCATCCAGGAGGGATGGCATTGATTTGAAGAAAGAGTCTTACCTCCGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatc-atagttgat-ttaacttatattt-ttcattgttgatgttaacttgttcctt-tcaatcattattatgatcttcaattaccatgatgcatgcattt
| || || || |||  |||||| || ||  | ||||||||| ||||| | || ||||| || || |||||| ||||||||||||||||| |  | ||||||||||| | | | ||| |   |   | |  |  || ||| | |     ||     |  |  | | |  | ||| |||   ||  ||||  |      || ||  
AATCGCCCTCAAGGTTGGATGGAATCGACATAAAGAAAGAGACTTACTTTCGGAAATCGTACTGCACTTTTTTACAAGATTTGGGCATGCGATTAAAAGTgtaagacccagacttggtgccagtctgtcctcatttattttagtcagcaatcaaattatggttagttttcattttga--ctctgttactctctgttttggat--

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|86904853|gb|CI310646.1|CI310646
EST:     CGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGT                         GCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCT
genomic: CGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcat ... tctgtggtagGCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCT
EST: gi|33674887|gb|CF303126.1|CF303126
EST:     CGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGT                         GCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCT
genomic: CGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcat ... tctgtggtagGCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCT
EST: gi|33675720|gb|CF303959.1|CF303959
EST:     CGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGT                         GCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCT
genomic: CGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcat ... tctgtggtagGCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCT
EST: gi|29677818|gb|CB674093.1|CB674093
EST:     CGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGT                         GCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCT
genomic: CGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcat ... tctgtggtagGCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCT
EST: gi|58668632|gb|CK057318.1|CK057318
EST:     CGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGT                         GCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCT
genomic: CGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcat ... tctgtggtagGCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCT

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), 73 (downstream exon)
Score: 40

ATTCTCCATCCAGGAGGGATGGCATTGATTTGAAGAAAGAGTCTTACCTCCGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcat ... tctgtggtagGCCACAAGTCACTATTGCTACAGCTATTGTGTTCTGTCACCGTTTTTACCTTCGTCAGTCCCATGCAAAAAATGATAGACGA




<











<


<