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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTCCATCCAGGAGGGATGGCATTGATTTGAAGAAAGAGTCTTACCTCCGAAAATCATATTGTACTTTTCTACAAGATTTGGGCATGAGGCTTAAAGTgtaagatcatagttgatttaacttatatttttcattgttgatgttaacttgttcctttcaatcattattatgatcttcaattaccatgatgcatgcattt...

Basic information

species Oryza sativa
transcript LOC_Os12g30020.1
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|58668632|gb|CK057318.1|CK057318
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