Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttctgaaccaactgaaatcgatgttatgttgacgtactatgttggtttttgttactttcctttaatataccctttgttgtctggtattaattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT

Basic information

species Oryza sativa
transcript LOC_Os02g53060.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g53060.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G374881_T02 (Zea mays), 3'ss of exon 1
atg-ttctgaaccaactgaaatcgatgttatgttgacgtactatgttg--gtttttgttactttcctttaatataccctttgttgtctggtattaattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT
 || || ||  ||   |     | |   ||  ||    || || | ||  || ||  ||| |||   ||     |     |    | |  |  |    || |||||||||||| || |||||||| || ||||||||||| ||  | || |||||||||||| | || ||||||||||||
-tgcttttgctcctgtttctgccaaa--taaatttcattattaagctgatgtattctttattttaaatttggccaagtgctaacatttcctgctccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT

upper sequence: LOC_Os02g53060.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 1
---atgttctgaaccaactgaaatcgatgttatgttgacgtactatgttggtttttgtt--actttcctttaatataccctttgttgtctggtattaattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT
    ||||   | | ||  ||| ||| | ||| | ||| ||| | | ||  ||| | ||   |       ||||||    | ||||| ||| |   |   || |||||||||||| || |||||||| || |||||||||||||| || || |||||||||||  |||| ||||||||||||
ctcctgtttccaccaaatagaattcgttattaagctgatgtagtct-ttattttctatttggccaagtgctaatat-ttttgtgttgcctgctccaa---ctcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT

upper sequence: LOC_Os02g53060.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G374881_T01 (Zea mays), 3'ss of exon 1
atg-ttctgaaccaactgaaatcgatgttatgttgacgtactatgttg--gtttttgttactttcctttaatataccctttgttgtctggtattaattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT-----------------------
 || || ||  ||   |     | |   ||  ||    || || | ||  || ||  ||| |||   ||     |     |    | |  |  |    || |||||||||||| || |||||||| || ||||||||||| ||  | || |||||||||||| | || ||||||||||||                       
-tgcttttgctcctgtttctgccaaa--taaatttcattattaagctgatgtattctttattttaaatttggccaagtgctaacatttcctgctccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTGTAAGTGTTGTTGTCTTCTAATG

upper sequence: LOC_Os02g53060.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G152775_T03 (Zea mays), 3'ss of exon 1
---atgttctgaaccaactgaaatcgatgttatgttgacgtactatgttggtttttgtt--actttcctttaatataccctttgttgtctggtattaattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT-----------------------
    ||||   | | ||  ||| ||| | ||| | ||| ||| | | ||  ||| | ||   |       ||||||    | ||||| ||| |   |   || |||||||||||| || |||||||| || |||||||||||||| || || |||||||||||  |||| ||||||||||||                       
ctcctgtttccaccaaatagaattcgttattaagctgatgtagtct-ttattttctatttggccaagtgctaatat-ttttgtgttgcctgctccaa---ctcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTGTAAGTGCCATTGTCTTCTAATG

upper sequence: LOC_Os02g53060.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G08200.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------------------------atgttctgaaccaactgaaatcgatgttatgttgacgtactatgtt--ggtttttgttactttcctttaatataccctttgttgtctggtatta--attcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT
                                                                                   ||  ||||    || |  || |    |  |||| | | | |  | |  | || | |||  |    | | |  ||   || ||||| |  | ||   | | | |||| ||||||| || ||||| || |||||||| || |||||||| ||||| ||||| ||| | || ||||||||||| 
gtacactctctttctcctttccaagccgatcccatattaatttagggttttcgttttttcttttgttttgttttgactgtttcattctctgggt-aattacaagct---tcttgtttaaggattgagattagattctcgttgttgatttgtgaagtaat-ttagttgtttattttttccactttcagGAGTGTATGTTGCCAACCGAGCATCGGACAAAATCACTCAGCTCACTGATAATGTATACGTGTGTCGCTCTGGATCG

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|88692730|gb|CI736305.1|CI736305
EST:     CTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCG                         GAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACA
genomic: CTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCGgtatgcctcg ... taattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACA
EST: gi|58685118|gb|CK073805.1|CK073805
EST:     CTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCG                         GAATGTCTGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACA
genomic: CTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCGgtatgcctcg ... taattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACA
EST: gi|88584075|gb|CI701601.1|CI701601
EST:     CTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCG                         GAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACA
genomic: CTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCGgtatgcctcg ... taattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACA
EST: gi|66924564|gb|CX111412.1|CX111412
EST:     CTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCG                         GAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACA
genomic: CTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCGgtatgcctcg ... taattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACA
EST: gi|88325048|gb|CI646464.1|CI646464
EST:     GCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCANNGCACCG                         GAATGTATGTGGCAAACCGCGCGTCGGACAAGAT-ACTCAGCTA-CTGAC
genomic: GCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCA--GCACCGgtatgcctcg ... taattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGAC
EST: gi|163920296|gb|EG710592.1|EG710592
EST:     CTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCG                         GAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACCGACA
genomic: CTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCGgtatgcctcg ... taattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACA
EST: gi|88338208|gb|CI633327.1|CI633327
EST:     CTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCG                         GAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACA
genomic: CTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCGgtatgcctcg ... taattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtttttgttactttcctttaatataccctttgttgtctggtattaattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT
                                          tattaat  putative branch site (score: 2)
                                                ttctt  CT-rich tract
             tttcctttaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttctgaaccaactgaaatcgatgttatgttgacgtactatgttggtttttgttactttcctttaatataccctttgttgtctggtattaattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT