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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTTCAAGTGTTGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtccttgataagactgttctcacacttgacaacgctgtatccatgtcctggttcctgatatcaatgttgccgccttcaacag

Basic information

species Oryza sativa
transcript LOC_Os01g70300.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70300.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G300862_T04 (Zea mays), 5'ss of exon 2
GCCTTTCAAGTGTTGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtcc-----ttgataagactgttct--cacacttgacaa-cgctgtatccatgtcctggttcctgatatcaatgttgccgccttcaacag---------------------------------------------------------------------------------------------------
 |    |  ||| |||||||||| ||||| ||||| ||||||||||||||||| || || |||||| |||     |||  |         |  |||||   |  |   ||   | | |||  ||| |  |   ||| ||| |  |    |||  ||                                                                                                   
ACGGGACGTGTGCTGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAGgtactccctcgcttgccagagtcaccatagcacaccaaatgagtactacgtgcttgt--tggcttgttgcatccatggt-tcttagtcacaagtcacaacatctatcatcaaaggaaaccaaattgagcaaaatttgtttgtcatatgcatgtttccggcaccgacatttaccacgccttcatcctgagcag

upper sequence: LOC_Os01g70300.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G700866_T02 (Zea mays), 5'ss of exon 13
GCCTTTCAAGTGTTGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtcc-----ttgataagactgttct--cacacttgacaa-cgctgtatccatgtcctggttcctgatatcaatg-ttgccgccttcaacag------------------------------------------------------------------------------------------
      || ||| |||||||||| ||| | ||||| ||||||||||||||||| || || |||||| |||     |||  |         |  |||||   |  |   ||   | | |||  ||| |  |   ||| ||| ||        |||||                                                                                           
ATGGGACATGTGCTGAGGAAAAGTGGGATTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAGgtactccctcgcttgccagagtcaccatagcacaccaaatgagtactacgtgcttgt--tggcttgttgcatccatggttcttagtcacaacatctatcatcaaaggaaaccaaattgagcaaaatttgtttgtcatatgcatgtttccggcaccaacattcaccacgtcttcatcctgagcag

upper sequence: LOC_Os01g70300.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G169046_T01 (Zea mays), 5'ss of exon 5
GCCTTTCAAGTGTTGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtcc-----ttgataagactgttct--cacacttgacaa-cgctgtatccatgt-----cctggttcctgatatcaatgttgccgccttcaacag--
      || ||| |||||||||| ||||| ||||| ||||||||||| ||||| || || |||||| |||     |||            |  |||||   |  |   ||   | | ||      ||| |     |   | |||       |||  || |   
---GGACATGTGCTGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCTCAAGGAGCGTCAAAGgtactccctcgcttgtcggagtcaccatagcacaccaaatgagtactacgtacttgagagcacctagaggggggggtgaataggtgatcctgtaaaactt

upper sequence: LOC_Os01g70300.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ34831 (Selaginella moellendorffii), 5'ss of exon 4
-------------------------------------GCCTTTCAAGTGTTGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtccttgataagactgttctcacac--ttgacaacgctgtatccatgtcctggttcctgatatcaatgttgccgccttcaacag
                                     |  ||    |||||   | |    ||  | || |||||||||||||| |||||||| |||||||||    ||  |     ||||||  | |  | ||| |  || |  |  || |                                   
TGGAAACGTGGAGCGCTCCTCCCTTGTGCTCAAGAAAGTTTTCTCGGTGTTTGAGGAGCTGGGAATCAAGGTCCAGATGATCTCACAAGGTGCTTCCAAGgtaaaagttcttccttttgttcttgctcgatcgaccatccttttgctttgacag---------------------------------

upper sequence: LOC_Os01g70300.1 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ06877 (Selaginella moellendorffii), 5'ss of exon 4
-------------------------------------GCCTTTCAAGTGTTGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtccttgataagactgttctcacac--ttgacaacgctgtatccatgtcctggttcctgatatcaatgttgccgccttcaacag
                                     |  ||    |||||   | |    || || || |||||||||||||| |||||||| |||||||||    ||  |     ||||||  | |  | ||| |  || |  |  || |                                   
TGGAAACGTGGAGCGCTCCTCCCTTGTGCTCAAGAAAGTTTTCTCGGTGTTTGAGGAGCTGGGAGTCAAGGTCCAGATGATCTCACAAGGTGCTTCCAAGgtaaaagttcttccttttgttcttgctcgatcgaccatccttttgctttgacag---------------------------------

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|88227424|gb|CI226904.1|CI226904
EST:     TGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAG                         GTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
genomic: TGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtccttg ... ccttcaacagGTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
EST: gi|55437244|gb|CV731821.1|CV731821
EST:     TGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAG                         GTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
genomic: TGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtccttg ... ccttcaacagGTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
EST: gi|66922023|gb|CX108871.1|CX108871
EST:     GCAAGGTGCATCCAAG                         GTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
genomic: GCAAGGTGCATCCAAGgtagtccttg ... ccttcaacagGTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
EST: gi|55437242|gb|CV731820.1|CV731820
EST:     TGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAG                         GTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
genomic: TGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtccttg ... ccttcaacagGTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
EST: gi|89180453|gb|CI044732.1|CI044732
EST:     TGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAG                         GTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
genomic: TGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtccttg ... ccttcaacagGTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
EST: gi|88907427|gb|CI090221.1|CI090221
EST:     TGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAG                         GTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
genomic: TGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtccttg ... ccttcaacagGTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
EST: gi|88283415|gb|CI404861.1|CI404861
EST:     GAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAG                         GTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG
genomic: GAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtccttg ... ccttcaacagGTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTTCAAGTGTTGAGGAAAAGCGGGGTGAATGTCCAGATGATCTCGCAAGGTGCATCCAAGgtagtccttgataagactgttctcacacttgacaacgctgtatccatgtcctggttcctgatatcaatgttgccgccttcaacag

- - - - - - - - - - - - - - - - - - CAGATG