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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGACACCAGTTCTTGTTGTTCTTCCTGTGTTGACGTTTTGGTTTTACAAGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtgacaggaagttttgtatactgaaatgtttgttttggtttggtggtaagagtgaaatttgttggatgtgcag

Basic information

species Oryza sativa
transcript LOC_Os05g51630.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51630.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G456000_T01 (Zea mays), 5'ss of exon 11
GACGACACCAGTTCTTGTTGTTCTTCCTGTGTTGACGTTTTGGTTTTACAAGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtgacaggaagttttgtat-actgaaatgtttgttttggtttggtggtaagagtgaaatttgttggatgtgcag---------
||||||||| || ||  |||||||||||||| |||| ||| ||||||||||||||||||||||||| |||||||| ||||| ||||||||||| || ||||||   |  | |  |   | |  ||  ||       ||     ||| ||  || | |   ||| || | |   || || |          
GACGACACCTGTGCTCCTTGTTCTTCCTGTGCTGACCTTTGGGTTTTACAAGTACTGCAAGAACCGCTTTGAGCCGGCATTCGTGAGGAACCCGCTGCAGgtatatttcgccgtggcatatgctaccacattgtcattgacgatggatt--tgctgaacatgatatatat-acatatgaaatggtggcag
















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|29666920|gb|CB663195.1|CB663195
EST:     AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|86538186|gb|CI178392.1|CI178392
EST:     AGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: AGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|29660844|gb|CB657119.1|CB657119
EST:     AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|218481681|gb|FG962994.1|FG962994
EST:     AGTACTGCAAGAACCGGTTTGAGCCTGCCTTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACATCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|86835886|gb|CI346081.1|CI346081
EST:     AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|88474517|gb|CI411788.1|CI411788
EST:     TGCATTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: TGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|29666876|gb|CB663151.1|CB663151
EST:     AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|88529999|gb|CI458362.1|CI458362
EST:     TTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: TTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|88502300|gb|CI429806.1|CI429806
EST:     AGCCTGCATTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: AGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|29678913|gb|CB675188.1|CB675188
EST:     AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|88501925|gb|CI429431.1|CI429431
EST:     TGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGGCAAGGGAGCCAACCTTCGA
genomic: TGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAAC-GGGCAAGGGAGCCAACCTTCGA
EST: gi|29627769|gb|CB632780.1|CB632780
EST:     AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|88487157|gb|CI424428.1|CI424428
EST:     GCCTGCATTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: GCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|88480824|gb|CI418095.1|CI418095
EST:     TTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: TTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|5607372|gb|AU076044.1|AU076044
EST:     GTACTGCAAGAACCGGTTTGAG-CTGCATTTGTGAGGAACCCANTTACAG                         GAANCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGA
genomic: GTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCA-CTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGA
EST: gi|88511172|gb|CI438678.1|CI438678
EST:     ACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: ACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|88524719|gb|CI453663.1|CI453663
EST:     TGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: TGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|88482848|gb|CI420119.1|CI420119
EST:     ACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: ACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|88837473|gb|CI078833.1|CI078833
EST:     AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT
EST: gi|89185677|gb|CI047546.1|CI047546
EST:     AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAG                         GAAGCGATGAGGAAAGACACCNTGGAACGGGCAAGGGAGCCAACCTTCGAT
genomic: AGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtg ... ggatgtgcagGAAGCGATGAGGAAAGACACCCTGGAACGGGCAAGGGAGCCAACCTTCGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGACACCAGTTCTTGTTGTTCTTCCTGTGTTGACGTTTTGGTTTTACAAGTACTGCAAGAACCGGTTTGAGCCTGCATTTGTGAGGAACCCACTACAGgtaatgtgtgacaggaagttttgtatactgaaatgtttgttttggtttggtggtaagagtgaaatttgttggatgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC