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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcacatcattgttcagtttgtcagcttgtttagatgctaggagtttagcacatgttaattggtctatctgactgatatactctttcattaaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA

Basic information

species Oryza sativa
transcript LOC_Os02g54340.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 2
------tttcacatcattgttcagtttgtcagcttgtttagatgctaggagtttagcacatgttaattggtctatctgactgatatactctttcattaaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA
      ||  |  |  || | || ||| |||| ||||||  |||||||||     |  | | | |||  |  || ||||  ||| |  ||||  | ||||| | ||| || ||||||||||| || ||| |||| ||||| ||||| |||||| | || |||||||| ||||||||||||||||| |||||| | |||
attttgttctatgttgttctgcaatttatcagtttgttttaatgctaggaa---ggtccttttgaatcagcatacctga--gatgtgttcttatactaaatgc-agGTATAAAGGAGTCTGATACAGGGTTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAACAGATGATGCAAGAAGAACAACCGTTACAA

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 2
-----tttcacatcattgttcagtttgtca-gcttgtttagatgctaggagtttagcacatgttaattggtctatctgactgatatactctttcattaaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA
      || | ||  || | | | |||||    |||    ||  ||| |   ||| ||| ||  ||     ||     | || ||  ||   | ||   |    ||| || ||||||||||| |||||  | ||| |||| ||||| |||||||| || || |||||||| |||||||| |||||||| || || || 
gttgcatttatatt-ttatgctgattgtcctaattgcacggaatctatgctgttaacacttgcaaac----ctcctcaaatgtta-gcttcctgatgttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 2
-tttcacatcattgttcagt--ttgtcagcttgtttagatgctaggagtttagcacatgttaattggtctatctgactgatatactctttcattaaatcc-cagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA
 | |      | ||||   |  |  | |  |||| | ||   |  |  |    | | |   | || || | |  || | |     | | |||    ||   |||| || || ||||| ||||| |||||||||   || || || |||||||| |||||||||||||||||||||||||| || |||||  |||| 
gtatgtaggaactgtttgatggtcctaatattgtgt-gacatttcgcttacctctctttccatttagtttctaagagtta---gttgtgtcacggcatgagcagGAATCAAAGAGTCCGACACCGGGCTGGCAGTGCCTAGTCAGTGGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAG

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 2
tttcacatcattgttcagtttgtcagcttgtttagatgctaggagtttagcacatgttaattggtctatctgactgatatactcttt-cattaaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA
                                                       ||   |||  | ||||  |||   |  | |   | |    | |||||||| |||||||| |||||||| || ||| | || ||||| |||||||| || || |||||||| ||||||||||||||||| || ||||||
-------------------------------------------------------gtgcgttg--cgatcttgctgggcttttttgagcgtgcttttccagGGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAA

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ13722 (Selaginella moellendorffii), 3'ss of exon 2
tttcacatcattgttcagtttgtcagcttgtttagatgctaggagtttagcacatgttaattggtctatctgactgatatactctttcattaaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA
                                          | |  | ||  || ||  | ||  | | |||      | || ||          |||||||| |||||||| |||||||| || ||| | || ||||| |||||||| || || |||||||| ||||||||||||||||| || ||||||
------------------------------------------gtgcgttgcg-attttgctgggcttttttga---gcgtgctttt----------ccagGGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAA

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|88302490|gb|CI668336.1|CI668336
EST:     GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTG                         GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
genomic: GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTGgtgagttaag ... taaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
EST: gi|58603359|gb|CK013887.1|CK013887
EST:     ATCAATGACCTTTGTG                         GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
genomic: ATCAATGACCTTTGTGgtgagttaag ... taaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
EST: gi|88372910|gb|CI640361.1|CI640361
EST:     GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTG                         GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
genomic: GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTGgtgagttaag ... taaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
EST: gi|29684844|gb|CB681119.1|CB681119
EST:     GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTG                         GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
genomic: GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTGgtgagttaag ... taaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
EST: gi|88310318|gb|CI659108.1|CI659108
EST:     GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTG                         GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
genomic: GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTGgtgagttaag ... taaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
EST: gi|58602175|gb|CK012703.1|CK012703
EST:     GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTG                         GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
genomic: GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTGgtgagttaag ... taaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
EST: gi|88388241|gb|CI627780.1|CI627780
EST:     GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTG                         GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
genomic: GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTGgtgagttaag ... taaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
EST: gi|88326660|gb|CI658382.1|CI658382
EST:     GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTG                         GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
genomic: GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTGgtgagttaag ... taaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
EST: gi|58675342|gb|CK064029.1|CK064029
EST:     GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTG                         GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
genomic: GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTGgtgagttaag ... taaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAG
EST: gi|88574346|gb|CI666115.1|CI666115
EST:     GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTG                         GGATTAAGGAGTCTGACACTGGGGCTGGGCACCACCCAGCCCATTGGGATC
genomic: GGTGGAGAAAGAAATAAAAGAAATGGCTAAGAAGATCAATGACCTTTGTGgtgagttaag ... taaatcccagGGATTAAGGAGTCTGACACTGGG-CTGG-CACCACCCAGCCAAT-GGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagcacatgttaattggtctatctgactgatatactctttcattaaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA
                          gactgat  putative branch site (score: 3)
                                    ctctttcatt  putative PPT
                                       tttcattaaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcacatcattgttcagtttgtcagcttgtttagatgctaggagtttagcacatgttaattggtctatctgactgatatactctttcattaaatcccagGGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA