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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttacaagtttatttctattgtttgtctcttatgtagaaattgaactttaatcatatggtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCA

Basic information

species Oryza sativa
transcript LOC_Os03g14980.2
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G550865_T02 (Zea mays), 3'ss of exon 7
----gttagt-tacaagtttattt-ctattgtttgtctcttatgtagaaattgaactttaatcat-atggtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCA
    || | | |  |   |||  | | |||  || | | || ||||||||   | |||| ||| | ||  | ||||||||| |||||||| ||||||||| | |||||||| ||||| |||||||| || || || |||||||||||||| || |||||||||||||||||||||||||
gttggtaaatctttacacttacatacaattagtttttttttttgtagaaac-aatctttgatctttatttttactgcagACAATGACAACATTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTTCACCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCA

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G030422_T03 (Zea mays), 3'ss of exon 22
-------gttagttacaagtttatttctattgtttgtctcttatgtagaaattgaactttaatcat-atggtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCA
         |  ||||| ||||  | | || |||  | | || | ||||||   | |||| ||| | ||  | ||||||||| |||||||| ||||||||| | |||||||| ||||| |||||||| || ||||| |||||||||||||| || |||||||||||||||||||||||||
gttggtaaatctttaca-gtttcatacaatagtt--ttttttttctagaaac-aatctttgatctttatttttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCA

upper sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 21
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
gttagttacaagtttatttctattgtttgtctcttatgtagaaattgaactttaatcatatggtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCA
              |||    ||| |||   ||||     |     ||||||    ||| |        |||  ||||||| | || ||||| ||||| || || |||||||| || ||||| || |||||||| ||||| || ||||| ||||||||||| || || || |
-------------gtatgcacatt-tttccttcttgaccggtgtaagaactt--gccatgtc-------cagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA

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|88348934|gb|CI653978.1|CI653978
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58658403|gb|CK047083.1|CK047083
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|88344056|gb|CI638791.1|CI638791
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58657128|gb|CK045808.1|CK045808
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58677432|gb|CK066119.1|CK066119
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58655231|gb|CK043911.1|CK043911
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58691548|gb|CK080235.1|CK080235
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58594272|gb|CF992580.1|CF992580
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58658854|gb|CK047534.1|CK047534
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58657970|gb|CK046650.1|CK046650
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTAGGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58656462|gb|CK045142.1|CK045142
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|88573729|gb|CI665498.1|CI665498
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|29680680|gb|CB676955.1|CB676955
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|163919897|gb|EG714407.1|EG714407
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAAC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAAC
EST: gi|58689471|gb|CK078158.1|CK078158
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|58694923|gb|CK083610.1|CK083610
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
EST: gi|29673860|gb|CB670135.1|CB670135
EST:     TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAG                         ACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC
genomic: TGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca ... gtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctattgtttgtctcttatgtagaaattgaactttaatcatatggtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCA
                                ctttaat  putative branch site (score: 4)
                        aaattgaactttaat  TA-rich tract