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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctatcccattacgatttcatttttcatttttctgccccctccccctccccctcactcactctctctctctctctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTC

Basic information

species Oryza sativa
transcript LOC_Os05g01060.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01060.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G104377_T02 (Zea mays), 3'ss of exon 1
------gtatcc-tatcccattacgatttcatttttcattttt------ctgccccctccccctccccctcactcactctctctctctctctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTC
      ||| |  | ||    | |   | | | |  || |||         | |  |  |     |     || ||      || | ||||||| |||||||||||||||||||||  | ||||||||||| |||||||||||||| |||||  ||||| | 
gtatcagtaccaatctcttcctgcctctgcctctgccaatttgagggaatcggctgcaactagaacaagcgacccatcactcctgtatctctct-tcagCTGGAGGAGAACAGCCGGTTGAAGGACGAGCTGATGCTCAAGACGCGGGAGCTCCACAGAATT
















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|88325639|gb|CI648076.1|CI648076
EST:     TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAG                         CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
genomic: TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAGgtatcctatc ... tctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
EST: gi|88302566|gb|CI668412.1|CI668412
EST:     TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAG                         CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
genomic: TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAGgtatcctatc ... tctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
EST: gi|88393943|gb|CI684210.1|CI684210
EST:     TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAG                         CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
genomic: TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAGgtatcctatc ... tctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
EST: gi|88372382|gb|CI619712.1|CI619712
EST:     TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGAAGCAG                         CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
genomic: TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAGgtatcctatc ... tctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
EST: gi|88409673|gb|CI568963.1|CI568963
EST:     TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAG                         CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
genomic: TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAGgtatcctatc ... tctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
EST: gi|88349232|gb|CI678207.1|CI678207
EST:     TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAG                         CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
genomic: TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAGgtatcctatc ... tctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
EST: gi|88358406|gb|CI606915.1|CI606915
EST:     TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCAC-ATCCGGCAGCAG                         CTGGAGGAGAACAGACGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
genomic: TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAGgtatcctatc ... tctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
EST: gi|88333795|gb|CI643827.1|CI643827
EST:     TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAG                         CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
genomic: TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAGgtatcctatc ... tctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
EST: gi|88429307|gb|CI690207.1|CI690207
EST:     TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAG                         CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTC
genomic: TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAGgtatcctatc ... tctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTC
EST: gi|88419574|gb|CI686791.1|CI686791
EST:     TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAG                         CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
genomic: TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAGgtatcctatc ... tctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
EST: gi|88310594|gb|CI672453.1|CI672453
EST:     TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAG                         CTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG
genomic: TCCAGGTGATGCGCGCCGTGGAGGACGCCGAGGCCACCATCCGGCAGCAGgtatcctatc ... tctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctgccccctccccctccccctcactcactctctctctctctctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTC
                          cactcac  putative branch site (score: 2)
        ccccctccccctcccc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctatcccattacgatttcatttttcatttttctgccccctccccctccccctcactcactctctctctctctctctctcagCTGGAGGAGAACAGCCGCCTCAAGGACGAGCTCATGCTCAAGACGCGAGAGCTTGACAGATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT