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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctcctttctaataccatttacatatattattcaggaaaatatgtgttgcatatgcacattcactagttcttacagagctcgctgaatggttttatgcagGTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGA

Basic information

species Oryza sativa
transcript LOC_Os01g23610.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 3
gctcctttctaataccatttacata-tattattcaggaaaatatgtgttgcatatgcacattcact-----agttcttacagagctcgctgaatggttttatgcagGTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGA
    | || | |||    || |||| ||    | |  ||   || ||||||   | |   |||| |     |   |||  | |||| ||   ||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||| ||||||||||| || ||||| |||||||||||||| |||||||||||
----ccttatcatatatgttgcatactacagctta--aatgcatttgttgccattcctatttcattctagcatccctttaaaagcttgcaccatggttttatgcagGTAAAACTGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGA

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 4
-------gctcctttctaataccatttacatatattattcaggaaaatatgtgttgcatatgcacattcactagttcttacagagctcgctgaatggttttatgcagGTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGA
         |  |  || ||||  |   |   | || ||| |     |   |  | | | |    || || || |      | ||||| |  | |   |  || |||| || || ||  |||| ||||| |||||||| ||||| ||| | |||||||| ||||| || || || ||||| ||||| ||||| || |||||||||||
ggggatctttgttcactgatactgtcc-ctcttgtttttctgttttgttatttcttcttcttggtat-cattaatg-----aaagctcaccaagtaaatgcattcagGAAAGACTGTGATTACCAGTGACCATGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGA

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 4
------gctcctttctaa-taccatttacatatattatt--caggaaaatatgtgttgcatatgcacatt----cactagttcttacagagctcgctgaatggttttatgcagGTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGA
      | |  | | ||| |   || |  |       ||  |   ||||     | | |  ||     ||     |  |  |     |    ||     ||  | |  |||||| || || ||  | || |||||||||||| | ||| | ||||| ||||||||||||||||| || || ||||| ||||| || || || || ||||||||
gtatgtgtttttgtataaatgatatgtgaaaggggagttgcctcaaaaaccaaagcttctcatttcttttagtatagcaagtaccctaatattcctcatattttgtgctgcagGAAAGACTGTTATCACAAGTGATCATGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGA

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 4
gctcctttctaataccatttacatatattattcaggaaaatatgtgttgcatatgcacattcactagttcttacagagct---cgctgaatggttttatgcagGTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGA
  | | || || | ||| |||  |  |  ||  |  | |  |  |  |  || |     ||     ||||  | |   ||   | |   ||  |    |||||| || || ||  |||| || |||||||| || ||||| ||||| |||||||| ||||| || || || ||||| ||||| ||||| || |||||||||||
--ttccttgta-ttccagttatctgcaaaatctataatatgaatttgtcaatcttttggtttttgtgttcaaagatttctaatcaccagataatgacttgcagGGAAGACTGTTATTACCAGCGATCATGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGA

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 4
gctcctttctaataccatttacatatat----tattcaggaaaatatgtgttgcatatgcacattcactagttcttacagagctcgctgaatggttt---tatgcagGTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGA
     |    || |  || ||  | |      | ||| | |  ||||  | ||||    |   ||    |||         |||  || ||     |   |||||||| || ||||| ||||| |||||||| ||  | ||  | ||||   |||| ||||||||||| ||||| || |||||||||||||| || || ||||||||
-----taggaaaaattatgtaggtgttgcccatgttctgaacgatata-gctgca-gcactgtttttgaagtgaacttgatgcttactcaaaaacctggttatgcagGAAAGACCGTTTTTACAAGTGATCACGCTTTGAAGTTAGAGTGGATTCCAGACTGGATTGCGATCGTTGGCAGCGGTTACATTGGTCTAGAGTTCAGTGA

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|58675783|gb|CK064470.1|CK064470
EST:     TATTGCAACGGGGTCTGTTCCTTTTGTCCCCAATGGCATCGACATAGATG                         GTAAAACCGTATTTACTAGTGATCATGCACTAAAAGTTGAGTCAGTTCCTG
genomic: TATTGCAACGGGGTCTGTTCCTTTTGTCCCCAATGGCATCGAAATAGATGgtaattactg ... ttttatgcagGTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTG
EST: gi|58684178|gb|CK072865.1|CK072865
EST:     TATTGCAACGGGGTCTGTTCCTTTTGTCCCCAATGGCATCGAAATAGATG                         GTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTG
genomic: TATTGCAACGGGGTCTGTTCCTTTTGTCCCCAATGGCATCGAAATAGATGgtaattactg ... ttttatgcagGTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcatatgcacattcactagttcttacagagctcgctgaatggttttatgcagGTAAAACCGTATTTACTAGTGATCATGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGA
                      ttcttac  putative branch site (score: 2)
                                             ttttat  TA-rich tract