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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