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

GTCTAGTGGTCTGCGGGAAGAGATGTGATTCTGTTGGCATCCCAGCACTCAGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatttgcataatctgtttgtattgttgttgttttgacgtatatctcgtgttcaaaataaatatatgcatttcattccctctttattaattgagagcagttttattttgaaatgattcacag

Basic information

species Oryza sativa
transcript LOC_Os01g09120.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09120.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G176506_T04 (Zea mays), 5'ss of exon 2
GTCTAGTGGTCTGCGGGAAGAGATGTGATTCTGTTGGCATCCCAGCACTCAGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatttgcataatctgt---ttgtattgttgt-----tgttttgacgtatatctcgtgttcaaaataa-atatatgcatttcattccctctttattaattgagagcagttttattttgaaatgattcacag
||||||||||| || ||||||||||||| ||  |||||||||||||||||||||| || ||||| || ||||| |||||||||||||| ||||||||||||||||||||||||||| | |||   || | |||||||     ||| | | | ||| | | ||||| |||| |   ||| | || ||||| |   ||| |||| |  |  |     | |||||||| |||| |||||
GTCTAGTGGTCAGCAGGAAGAGATGTGACTCGATTGGCATCCCAGCACTCAGTTCGTCGTTAAAACTCTCTCTCGGTAGAATCAAACAGAGCTTTGTATTgtgagttatttgcatattttgtccattattttgttgtctacttgtctcgtcttat-ttttgtgttgaaaacattgtatgtccaattcatgcgtgcttcattattaaactg----atcattttgaactgat-cacag

upper sequence: LOC_Os01g09120.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G176506_T07 (Zea mays), 5'ss of exon 2
-------------------------GTCTAGTGGTCTGCGGGAAGAGATGTGATTCTGTTGGCATCCCAGCACTCAGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatttgcataatctgt---ttgtattgttgt-----tgttttgacgtatatctcgtgttcaaaataa-atatatgcatttcattccctctttattaattgagagcagttttattttgaaatgattcacag
                         ||||||||||| || ||||||||||||| ||  |||||||||||||||||||||| || ||||| || ||||| |||||||||||||| ||||||||||||||||||||||||||| | |||   || | |||||||     ||| | | | ||| | | ||||| |||| |   ||| | || ||||| |   ||| |||| |  |  |     | |||||||| |||| |||||
CTGAACAGCTACAGCAAGCTAACTGGTCTAGTGGTCAGCAGGAAGAGATGTGACTCGATTGGCATCCCAGCACTCAGTTCGTCGTTAAAACTCTCTCTCGgtagaatcaaacagagctttgtattgtgagttatttgcatattttgtccattattttgttgtctacttgtctcgtcttat-ttttgtgttgaaaacattgtatgtccaattcatgcgtgcttcattattaaactg----atcattttgaactgat-cacag

upper sequence: LOC_Os01g09120.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G02600.5 (Glycine max), 5'ss of exon 2
GTCTAGTGGTCTGCGGGAAGAGATGTGATTCTGTTGGCATCCCAGCACTCAGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatttgcataatctgtttgtattgttgttgttttgacgtatatctcgtgttcaaaataaatatatgcatttcattccctctttat-taattgagagcagttttattttgaaatgattcacag
|   | |||| ||  | ||||| |       |  || | |        | ||  | || || | | |||||||||||||||||||||||||||||||||||||||||||| | |   |||  ||   ||||| ||  |||  || |    |  || |     |   |  |  |  || |||   | ||| | | |||  |||   ||  ||   |             
GGAGATTGGTGTGTAGAAAGAGGTCCAGCATTCCTGACGTGGGTCTTTTAAGCACATCCTTGATTATTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttattggaaatgtctagtt---ttgttattactttaccgcaagctttatgct-----tttttgcagacccttaatttgttgtttgtatgattttgagt--ttccatgcag-------------

upper sequence: LOC_Os01g09120.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA16G10260.1 (Glycine max), 5'ss of exon 4
GTCTAGTGGTCTGCGGGAAGAGATGTGATTCTGTTGGCATCCCAGCACTCAGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatttgcataatctgtttgtattgttgttgttttgacgtatatctcgtgttcaaaataaatatatgcatttcattccctctttat-taattgagagcagttttattttgaaatgattcacag
    | |||| ||  | ||||| |       |  || | |        | ||  | || || | | |||||||||||||||||||||||||||||||||||||||||||| | |   |||  ||   ||||| ||  ||   || |    |  || |     |   | ||  |  || |||   | ||| | | |||  |||   ||  || | |             
-GAGATTGGTGTGTAGAAAGAGGTCCAGCATTCCTGACGTGGGTCTTTTAAGCACATCCTTGATTATTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttattggaaatgtctagtt---ttgttattacttgaccgcaagctttatgct-----tttttgtagacccttaatttgttgtttgtatgattttgagt--ttccatgtag-------------

upper sequence: LOC_Os01g09120.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA01G04920.1 (Glycine max), 5'ss of exon 2
GTCTAGTGGTCTGCGGGAAGAGATGTGATTCTGTTGGCATCCCAGCACTCAGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatttgcataatctgtttgtattgttgttgttttgacgtatatctcgtgttcaaaataaatatatgcatttcattccctctttattaattgagagcagttttattttgaaatgattcacag
|   | |||| ||    ||||||||      |  ||   |        | ||  | || || | | ||||||||||||||||||||||||||||||||||||||||| || | |   |||  || | || ||  | ||                       | ||   ||||| || |     | ||| |||  |||      || | |||||||  |   |  |||
GCAGATTGGTGTGTCAAAAGAGATGCAGCATTCCTGATGTGGGTCTTTTAAGCACATCCTTGATTATTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttgttggaaatgtctagttttgttattacttttcc---------------------acaagcttatgctttccgcagacccttaatttgttgc---ttgtatgattttgagtttccttgcag

upper sequence: LOC_Os01g09120.2 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G02710.3 (Arabidopsis thaliana), 5'ss of exon 2
GTCTAGTGGTCTGCGGGAAGAGATGTGATTCTGTTGGCATCCCAGCACTCAGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatttgcataatctgtttgtattgttgttgttttgacgtatatctcgtgttcaaaataaatatatgcatttcattccctctttattaattgagagcagttttattttgaaatgattcacag
||  | | |||||||| ||| | |     |     ||  |       || || || || |||  | ||||||| ||||||||||||||||| || |||||||||||      ||| || | ||| |  |||| | |  ||   || |         |  |  |  ||||   ||||    ||     ||   |                                  
GTAGATTAGTCTGCGGAAAGCGGTACTGCTTGCGAGGAGTAGATTGTCTAAGCTCGTCGTTAGTTATTTCTCTCGGTAGAATCAAACAAAGTTTCGTATTgtgagt-----acattatttttttattgtgttatggagttacagtctgc--tacaatagattttgatattgacattgttctcgtaactttgcag---------------------------------

upper sequence: LOC_Os01g09120.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv01s0026g01590.t01 (Vitis vinifera), 5'ss of exon 3
GTCTAGTGGTCTGCGGGAAGAGATGTGATTCTGTTGGCATCCCAGCACTCAGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatttgcataatctgtttgtattgttgttgttttgacgtatatctcgtgttcaaaataaatatatgcatttcattccctctttattaattgagagcagttttattttgaaatgattcacag
|   | |||||||||  ||||||||    |    ||| ||       ||  || |||| |||| | | ||||||||||||||||||||||||||||||||||||||| ||   | |||   |   | || || |    | || ||  || | |||||  ||     |  |||  ||    |    | |     |           ||  | ||| |           
GCAAATTGGTCTGCGAAAAGAGATGCACCTTATCTGGAATTGGCCTCCTTGGTGCTTCCTTAATTATATCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttttt---acaattcctaaat-ttcttttaccatagatgtcaatatagtgtttgaagatggttaatgtcttcgccttatgcatcccacaacatatatgtgttgctcttgcag----------

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|29660689|gb|CB656964.1|CB656964
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29660992|gb|CB657267.1|CB657267
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29657673|gb|CB653948.1|CB653948
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29680769|gb|CB677044.1|CB677044
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29662742|gb|CB659017.1|CB659017
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|31818552|gb|CD645551.1|CD645551
EST:     AGTTCTTCATTAAATCTTTCTCTCGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29640574|gb|CB645583.1|CB645583
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29655805|gb|CB652080.1|CB652080
EST:     AGTTGTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GGCTGACCCCCATTTGCCTGACATGCCGATCATGTATGGTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|14571448|gb|BI118816.1|BI118816
EST:     AGTTCTTCATTAAATCTTTCTCTCGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|38474285|gb|CF958417.1|CF958417
EST:     AGTTCTTCATTAAATCTTTCTCTCGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|88228766|gb|CI228246.1|CI228246
EST:     CAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: CAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
EST: gi|29660961|gb|CB657236.1|CB657236
EST:     AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATT                         GACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT
genomic: AGTTCTTCATTAAATCTTTCTCTTGGTAGAATCAAACAAAGCTTTGTATTgtgagttatt ... tgattcacagGACTGACCCCCATTTGCCTGACATGCCGATCATCTATGCTAGTGATGCTTT