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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctagctaaggcgatcatcgttgtaggataagtgcagtgttgttttattgccttacctactgtcaccagtgaatcatcgtctgcttttttttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTCGGAATCAGCACTGTGTATTTGGGATTTGCATCTGTTTGCGCTCTTGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g04190.3
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04190.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G098011_T01 (Zea mays), 3'ss of exon 13
tctagctaaggcgatcatcgttgtag--gataagtgcagtgttgttttattgccttacctactgtcaccagtgaatcatcgtctgcttttttttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTCGGAATCAGCACTGTGTATTTGGGATTTGCATCTGTTTGCGCTCTTGCTG
 || | |||| ||| ||      ||    |  | |  |   | | |||| |  | ||     |     |  | |        ||| |||| |||||   ||||| || ||||| ||||||||||| ||||||||||| || |||||||| || || ||||||| ||| ||||||||||||||||| || ||||  ||||| |
-ctgg-taagacgaacactaccataattaagtaattaaccttggctttacttacatataccattgagtccttcacctggttcctggttttctttttcttcagGTATCCAACTTTTTTATTGGCCTGTACTTCTTGAGTGTTGTCAACAAGTTTGGGATCAGCAATGTATATTTGGGATTTGCATCAGTGTGCGTCCTTGCAG

upper sequence: LOC_Os01g04190.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 13
--tctagctaaggcgatcatcgttgtaggataagtgcagtgttgttttattgccttacctactgtcacc-agtgaatcatcgtctgcttttttttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTCGGAATCAGCACTGTGTATTTGGGATTTGCATCTGTTTGCGCTCTTGCTG
    ||  |      | ||  ||   | |  |  | |    | ||  || |||  ||   ||| ||| | | || | | || |    |||    ||    ||| | || |||||  | ||||| || |||||||||||||| || ||||| ||||| |||||||| || || ||||||||| || | || ||   ||||||||
gaagtactttctaaaaacactgtcaaatggaagtttcttcatggtgctaatgcagtag--actttcatctaatggaacttcatg-attttcccattgtatcagATCTCAAACTTTGTGATTGGGCTTTACTTCTTGAGCGTTGTAAACAAGTTCGGGATCAGCACAGTTTACTTGGGATTTTCAGCCGTCTGTCTTCTTGCTG
















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|163921085|gb|EG710424.1|EG710424
EST:     CCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCTCTGGGCATGCACTGG                         GTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTC
genomic: CCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCTCTGGGCATGCACTGGgtaagttatg ... ttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTC
EST: gi|38481055|gb|CF965144.1|CF965144
EST:     CCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCTCTGGGCATGCACTGG                         GTTTCGAACTTCTTTATTG
genomic: CCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCTCTGGGCATGCACTGGgtaagttatg ... ttttgggcagGTTTCGAACTTCTTTATTG
EST: gi|58598313|gb|CK008841.1|CK008841
EST:     CCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCTCTGGGCATGCACTGG                         GTTTCGAACTTCTTTATTGGGCTCTACTTCTTGAGCG
genomic: CCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCTCTGGGCATGCACTGGgtaagttatg ... ttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCG
EST: gi|27554385|gb|CA998285.1|CA998285
EST:     CCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCTCTGGGCATGCACTGG                         GTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCG
genomic: CCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCTCTGGGCATGCACTGGgtaagttatg ... ttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCG
EST: gi|27576947|gb|CA999641.1|CA999641
EST:     CCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCTCTGGGCATGCACTGG                         GTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTC
genomic: CCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCTCTGGGCATGCACTGGgtaagttatg ... ttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgccttacctactgtcaccagtgaatcatcgtctgcttttttttttgggcagGTTTCGAACTTCTTTATTGGCCTCTACTTCTTGAGCGTCGTCAACAAATTCGGAATCAGCACTGTGTATTTGGGATTTGCATCTGTTTGCGCTCTTGCTG
    gccttac  putative branch site (score: 3)
                            tcatcgtctgcttttt  putative PPT
                                       tttttttttt  TA-rich tract