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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGCACGCTCAAGAGAGTAGGTGTCAACACCATCCCCGCGATCGAGGAGGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcatccctcctgttttgcctaccgtaccatggaaatgccaactgcttcttggtgttagattacttatccatgttcgatccgacctgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g63400.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63400.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G023242_T05 (Zea mays), 5'ss of exon 3
CAGAGCACGCTCAAGAGAGTAGGTGTCAACACCATCCCCGCGATCGAGGAGGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataa-gcatccctcctgtt----ttgcctaccgtaccatg-----gaaatgccaactgcttcttggtgttagattacttatcc-atgttcgat--ccgacctgtgcag
||| |||| |||||||||||||| |||||||||||||| || ||||||||||| ||||| |||||||| |||||||||||||||||| | || |||||||||||    |  |  | ||||      || | || ||  ||||     |||  |       | |  || | |    |  |||| |  |||||   |   |  ||  |||||
CAGGGCACTCTCAAGAGAGTAGGGGTCAACACCATCCCTGCAATCGAGGAGGTGAACATATTCAAGGACGATCTCGTCATCCAGTTCTTGAACCCCAAAGgtatgccacccctgttctgtcgttactggccactgttacatgtttccgaagcgggggaatcctggtgttatcgactggcttagctgatgttttgtgctctgccgatgcag

upper sequence: LOC_Os03g63400.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EDO98665 (Chlamydomonas reinhardtii), 5'ss of exon 2
CAGAGCACGCTCAAGAGAGTAGGTGTCAACACCATCCCCGCGATCGAGGAGGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgta--taagcatccctcctgttttgcc--taccgtaccatggaaatgccaactgcttcttggtgttagattacttatccatgttcgatccgacctgtgcag
|| | ||| |||||| |  | || || |||||||||||||  ||||||||||| ||||| |||||||||||   |||||| || ||||| || ||||| |||   |  | |      | |      |    | |  || ||  | ||||| | |      ||       | ||    | ||||| | |||   | |     
CAAAACACCCTCAAGCGCCTGGGCGTGAACACCATCCCCGGCATCGAGGAGGTTAACATTTTCAAGGATGACAGCGTCATTCACTTCGTGAACCCCAAGGgtgggtccgaaaggaagcaggggcagcagcgcagggccgtgagagtgccagccggg----ggctccgtctcacggcactatgtttgctcctcgcag-----

upper sequence: LOC_Os03g63400.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S28_196V6.1 (Physcomitrella patens), 5'ss of exon 3
CAGAGCACGCTCAAGAGAGTAGGTGTCAACACCATCCCCGCGATCGAGGAGGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcatccctcctgttt---tgcctaccgt-accatggaaatgccaactgcttcttggtgttagat-tacttatccatgttcgat-ccgacctgtgcag-----------------------------
||||||||  | ||| || | || || |||||||| ||||  || || ||||| ||||||||| |||||||   ||||||||| ||||| || |||||||||||      || |    |||   ||  |   || ||| ||| |  |   |       | | | | |||| ||| |    |     ||        |||||                               
CAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAGGTTAACATCTTCCAGGATGAATCCGTCATCCACTTCGTTAACCCCAAAGgtatgcattcccttgaaatttgactggtttttgtgaccttgggagagattataaaagttcgct-tcagatgtacatccttacaccagacatttgagtgtgcttatcaaccgccccaactgatatgtgtgcag

upper sequence: LOC_Os03g63400.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ21066 (Selaginella moellendorffii), 5'ss of exon 2
CAGAGCACGCTCAAGAGAGTAGGTGTCAACACCATCCCCGCGATCGAGGAGGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcatccctc-ctgttttgcctaccgtaccatggaaatgccaactgcttcttggtgttagattacttatccatgttcgatccgacctgtgcag
|| | ||||||||||||| | || ||||||||||||||||  || |||||||| || ||||||||||| |||  |||||| || |||||||||||||||||||  |       || |||  | | | |  |       | | | |    |   ||||   |                                     
CAAAACACGCTCAAGAGATTGGGCGTCAACACCATCCCCGGCATTGAGGAGGTGAATATCTTCAAGGACGATACCGTCATTCACTTCGTCAATCCCAAAGgtaagaatggaaatctctgcgtggacgaatggtttgatggatttcttcttctatcttttcgcag----------------------------------

upper sequence: LOC_Os03g63400.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ19435 (Selaginella moellendorffii), 5'ss of exon 2
CAGAGCACGCTCAAGAGAGTAGGTGTCAACACCATCCCCGCGATCGAGGAGGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcatccctc-ctgttttgcctaccgtaccatggaaatgccaactgcttcttggtgttagattacttatccatgttcgatccgacctgtgcag
|| | ||||||||||||| | || ||||||||||||||||  || |||||||| || ||||||||||| |||  |||||| || |||||||||||||||||||  |       || |||  | | | |  |       | | | |    |   ||||   |                                     
CAAAACACGCTCAAGAGATTGGGCGTCAACACCATCCCCGGCATTGAGGAGGTGAATATCTTCAAGGACGATACCGTCATTCACTTCGTCAATCCCAAAGgtaggaatggaaatctctgcgtggacgaatggtttgatggatttcttcttctatcttttcgcag----------------------------------

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|88205126|gb|CI204975.1|CI204975
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|88209060|gb|CI208909.1|CI208909
EST:     AACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: AACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|38477612|gb|CF961745.1|CF961745
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|55409416|gb|CV721792.1|CV721792
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|8528376|gb|AU093191.1|AU093191
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|86824271|gb|CI260854.1|CI260854
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|86823386|gb|CI256364.1|CI256364
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|87015910|gb|CI279662.1|CI279662
EST:     TCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: TCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|425823|gb|D22501.1|D22501
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGGCGGANACACATGGGTGGTCAGT
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGT
EST: gi|86594523|gb|CI253422.1|CI253422
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAAA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|426706|gb|D22776.1|D22776
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|88977134|gb|CI024871.1|CI024871
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|3760604|gb|C97858.1|C97858
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|58597162|gb|CK007690.1|CK007690
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|86489014|gb|CI131647.1|CI131647
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|55440624|gb|CV733623.1|CV733623
EST:     ATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: ATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|86542346|gb|CI182552.1|CI182552
EST:     GGTCTACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
EST: gi|86821488|gb|CI266864.1|CI266864
EST:     GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAG                         TGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA
genomic: GGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcat ... acctgtgcagTGCAAGCTTCCATCGCCGCAAACACATGGGTGGTCAGTGGCTCCCCACAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAGCACGCTCAAGAGAGTAGGTGTCAACACCATCCCCGCGATCGAGGAGGTCAACATCTTCAAGGATGATCTCGTCATCCAGTTCGTCAATCCCAAAGgtataagcatccctcctgttttgcctaccgtaccatggaaatgccaactgcttcttggtgttagattacttatccatgttcgatccgacctgtgcag

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