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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatatgaggaattgataagctgcaagcttattaatagattgtgttaatacttgcattatttgtcaacctgttttgagatctaccctgtttatggttgcagATCATGTTACTCTTAACTTTGCAAGAAGTGGGGGGGCTGGTGGTCAGAATGTCAATAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g14510.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G170532_T01 (Zea mays), 3'ss of exon 1
------------gatatgaggaattgataagctgcaagcttattaatagattgtgttaatacttgcattatttgtcaacctgttttgagatctaccctgtttatggttgcagATCATGTTACTCTTAACTTTGCAAGAAGTGGGGGGGCTGGTGGTCAGAATGTCAATAAAG
              | | | ||| ||||    || ||  | ||||  |  ||   ||| | ||||    |||||  ||  | | ||   ||     |  ||||    |||||||||||||||| |||| |||||||||||||| ||  |||||||||||||||| || ||||
gatatattttccagtgttatgaaatgattt-ttgaaacttgattaccatgtttatttagtgcttg----atttgctaaagtttattctaatt----ccatttac---tgcagATCATGTTACTGTTAATTTTGCAAGAAGTGGTGGTCCTGGTGGTCAGAATGTTAACAAAG

upper sequence: LOC_Os03g14510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G14410.1 (Glycine max), 3'ss of exon 1
gatatgaggaattgataagctgcaagcttattaatagattgtgttaatacttgcattatttgtcaacctgttttgagatctaccctgtt-tatggttgcagATCATGTTACTCTTAACTTTGCAAGAAGTGGGGGGGCTGGTGGTCAGAATGTCAATAAAG
|  |     |  |     |   | |  ||   |||| ||      |||| |   |  |   |  ||      |||   | |    | |  | ||||| |||||||||||||  | | |||||| |||||||| ||  |||| |||||||||||||||||||
gccaaccttatatcccttgtcaccaattttcaaata-ataaccaaaatattaaaaagaaaagagaaatgtaattgcttttttttttttggtttggtttcagATCATGTTACGGTGAGCTTTGCCAGAAGTGGAGGACCTGGGGGTCAGAATGTCAATAAAG

upper sequence: LOC_Os03g14510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G03930.1 (Glycine max), 3'ss of exon 1
gatatgaggaattgataagctgcaagcttattaa-tagattgtgttaatacttgcattatttgtcaacctgttttgagatctaccctgtttatggttgcagATCATGTTACTCTTAACTTTGCAAGAAGTGGGGGGGCTGGTGGTCAGAATGTCAATAAAG
                              |||  |   || |||   | |||  || |||| ||||    || |    | |    || || ||||| |||||||||||||  | | |||||| |||||||| ||  |||| |||||||||||||||||||
-----------------------------gttaggtcccttatgtctcttctt--atcatttttcaaataattat----tttgttttggtt-tggtttcagATCATGTTACGGTGAGCTTTGCCAGAAGTGGAGGACCTGGGGGTCAGAATGTCAATAAAG

upper sequence: LOC_Os03g14510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0241g00090.t01 (Vitis vinifera), 3'ss of exon 2
---------gatatgaggaattgataagctgcaagcttattaatagattgtgttaatac-ttgcattatttgtcaacctgttttgagatctaccctgtttatggttgcagATCATGTTACTCTTAACTTTGCAAGAAGTGGGGGGGCTGGTGGTCAGAATGTCAATAAAG
         | | |||| | |||| || |    |  |   ||||  |||   |||   | ||    ||  |  ||   | |||| |  | |         ||  || |||| ||||||||| | |  |||||||||||||| ||| |||| |||||||||||||| ||||
gattaagatgctgtgagca-ttga-aaaccatgatatctataatcaattacattagctcgttaagctaagtaccattttattttcaattat--------catcatttcagACCATGTTACTGTGAGTTTTGCAAGAAGTGGTGGGCCTGGAGGTCAGAATGTCAACAAAG

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|88569683|gb|CI660858.1|CI660858
EST:     GAGCGCGCCGCTTCGGCCGGCTCCGACCCCCGCCCCCAAGATCACTTTGG                         ATCATGTTACTCTTAACTTTGCAAGAAGTNNNNNNNCTGGTGGTCAGAATG
genomic: GAGCGCGCCGCTTCGGCCGGCTCCGA-CCCCGCCCCCAAGATCACTTTGGgtaataatct ... atggttgcagATCATGTTACTCTTAACTTTGCAAGAAGTGGGGGGGCTGGTGGTCAGAATG
EST: gi|86831211|gb|CI297480.1|CI297480
EST:     GGAGCGCGCCGCTTCGGCCGGCTCCGACCCCGCCCCCAAGATCACTTTGG                         ATCATGTTACTCTTAACTTTGCAAGAAGTNNNNNNNCTGGTGGTCAGAATG
genomic: GGAGCGCGCCGCTTCGGCCGGCTCCGACCCCGCCCCCAAGATCACTTTGGgtaataatct ... atggttgcagATCATGTTACTCTTAACTTTGCAAGAAGTGGGGGGGCTGGTGGTCAGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatacttgcattatttgtcaacctgttttgagatctaccctgtttatggttgcagATCATGTTACTCTTAACTTTGCAAGAAGTGGGGGGGCTGGTGGTCAGAATGTCAATAAAG
 tgttaat  putative branch site (score: 3)
         attatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatatgaggaattgataagctgcaagcttattaatagattgtgttaatacttgcattatttgtcaacctgttttgagatctaccctgtttatggttgcagATCATGTTACTCTTAACTTTGCAAGAAGTGGGGGGGCTGGTGGTCAGAATGTCAATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG