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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtcagaataatttgtaaattagcaaagtaacccaggttcggaagttacaacatgctactagagtcaccttggccttactgtatctaatttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGATCTAGCTGAAGAAATTCTGCAGTTGTCTAAG

Basic information

species Oryza sativa
transcript LOC_Os05g03820.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 12
-----ttttgtcagaataatttgtaaattagcaaagtaacccaggttcggaagttacaacatgctactagagtcaccttggccttactgtatctaatttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGATCTAGCTGAAGAAATTCTGCAGTTGTCTAAG
     |||| | |  ||| | |    ||||||||  |  | |  ||  | ||   | ||  | | |  | | | |  |  |  || |||| | ||  ||| | |||||||    || ||||||||||| || || || |||||||||||||||||| ||||||| ||| ||||  |  || | |||
gattttttttttaccatattcttgtgattagcaac-tggctcttgta-gaaaagaataaagt-ccagcatatttaa-tcagttttgctgtgt-tatattggtcagGTACCATCGACTGGTTTGAAGACGCCGTTTCGTGATGGATATGTAAGAGATTTAGCTGAGGAAGTTCTAAAACTGGCCAAG
















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|29677971|gb|CB674246.1|CB674246
EST:     ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAG                         GTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
genomic: ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAGgtatcttgag ... atttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
EST: gi|88723315|gb|CI746825.1|CI746825
EST:     ACATGACCTCTGATTGGACAAATGAAGAAAGAGAAATGCTAAGGCGAAAG                         GTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
genomic: ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAGgtatcttgag ... atttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
EST: gi|11442624|gb|BF430527.1|BF430527
EST:     ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAG                         GTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
genomic: ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAGgtatcttgag ... atttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
EST: gi|29645922|gb|CB650929.1|CB650929
EST:     ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAG                         GTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
genomic: ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAGgtatcttgag ... atttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
EST: gi|2311262|gb|C27417.1|C27417
EST:     ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAG                         GTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
genomic: ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAGgtatcttgag ... atttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
EST: gi|58663354|gb|CK052040.1|CK052040
EST:     ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAG                         GTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
genomic: ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAGgtatcttgag ... atttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
EST: gi|2311714|gb|C27869.1|C27869
EST:     GGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAG                         GTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
genomic: GGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAGgtatcttgag ... atttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
EST: gi|58695197|gb|CK083884.1|CK083884
EST:     ACATGACCTCTGATTGGACAAATGAGGAACGAGAAATGCTAAGGCGAAAG                         GTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
genomic: ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAGgtatcttgag ... atttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
EST: gi|33676123|gb|CF304362.1|CF304362
EST:     ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAG                         GTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
genomic: ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAGgtatcttgag ... atttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
EST: gi|86900529|gb|CI298364.1|CI298364
EST:     ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAG                         GTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT
genomic: ACATGACCTCTGATTGGACAAATGAGGAAAGAGAAATGCTAAGGCGAAAGgtatcttgag ... atttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttacaacatgctactagagtcaccttggccttactgtatctaatttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGATCTAGCTGAAGAAATTCTGCAGTTGTCTAAG
                                        atctaat  putative branch site (score: 3)
                                       tatctaatttgatta  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtcagaataatttgtaaattagcaaagtaacccaggttcggaagttacaacatgctactagagtcaccttggccttactgtatctaatttgattagGTACCTGTAACCGGTTTGAAGACACCCTTCCGGGATGGATATGTAAGAGATCTAGCTGAAGAAATTCTGCAGTTGTCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG