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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggaccaaggcgtgaacttctacacttgatagatcttcatattctttaaccccagtaatccactgcttgttatcttagtgcacaccttattgcatccagGGTTTTGTTGAGGACCAATTTGGCCTTGGGTTGATTGCTCGGGCTGTTGAAGAAGGGATATCAGTCATAAAGCCTATGGGTATTATGATATTTAACATGG

Basic information

species Oryza sativa
transcript LOC_Os05g01470.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G098039_T01 (Zea mays), 3'ss of exon 4
----taggaccaaggcgtgaacttctacacttgatagatcttcatattctttaaccccagtaatccactgcttgttatcttagtgcacaccttattgcatccagGGTTTTGTTGAGGACCAATTTGGCCTTGGGTTGATTGCTCGGGCTGTTGAAGAAGGGATATCAGTCATAAAGCCTATGGGTATTATGATATTTAACATGG
     | ||  |    |   | | ||||| | ||   || |   |  |     |      |  ||   |   | ||  |    |  | | |||  ||||||||||||||||| |||||||||||||||||||||||||||||||| || || |||||||||||||| ||||||||||||   ||||||||| |||| |||||||
gttaaatgattattcagaccaatcctacattaga---atttctttgcttaaggattttgattttcttttatgt-ttgccaacatcgatatctttctgcatccagGGTTTTGTCGAGGACCAATTTGGCCTTGGGTTGATTGCTCGTGCGGTGGAAGAAGGGATATCTGTCATAAAGCCTTCAGGTATTATGGTATTCAACATGG

upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 4
------taggaccaaggcgtgaacttctacacttgatagatcttcatattctttaaccccagtaatccactgcttgttatcttagtgcacaccttattgcatccagGGTTTTGTTGAGGACCAATTTGGCCTTGGGTTGATTGCTCGGGCTGTTGAAGAAGGGATATCAGTCATAAAGCCTATGGGTATTATGATATTTAACATGG
      |     |||      || || | || |||    || ||| |     || |   ||  ||| ||    || | |  ||     |     | ||  ||| |||||||||| ||||||||||||||| | || || |||||| |||| ||||| || |||||| |||| || || || |  || |||||||| ||||||||||
gggatcttttggcaatatagaaattttttcaattgccttattttc-tgcctgtttatgacatgaatgcagca-ttctcacatt----tattttgtcttttatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAACATGG

upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 4
-taggaccaaggcgtgaacttctacacttgatagatcttcatattctttaaccccagtaatccactgcttgttatcttagtgcacaccttattgcatccagGGTTTTGTTGAGGACCAATTTGGCCTTGGGTTGATTGCTCGGGCTGTTGAAGAAGGGATATCAGTCATAAAGCCTATGGGTATTATGATATTTAACATGG
 |     |||      ||    |  | |||    || ||| |     || |   ||  ||| ||    |       ||| |       || ||||||| |||||||||| ||||||||||||||| | || || |||||| |||| ||||| || |||||| |||| || || || |  || |||||||| ||||| ||||
cttttggcaaaatagaaatgcttttaattgccttattttc-tgcctatttatgacatgaatgcagcattctcacatttattttgtcttttgttgcatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAATATGG

upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 4
-----taggaccaaggcgtg-aacttctacacttgatagatcttcatattctttaaccccagtaatccactgcttgttatcttagtgcacaccttatt-gcatccagGGTTTTGTTGAGGACCAATTTGGCCTTGGGTTGATTGCTCGGGCTGTTGAAGAAGGGATATCAGTCATAAAGCCTATGGGTATTATGATATTTAACATGG
     |    | ||   ||| || |  || ||  | ||   ||  | | | | | |     |  || | || | |||   | |  || |     |||    || |||||||||||||| || || |||||| | || ||||||||  | || ||||||||||| ||||| ||||| || |||   || |||||||||||||||||||
ttaatttactctaaaaggtgtaaatgatagaccaggta---ctggaaactttgttaaagtgg--atgctctacctgt--gcctgatgaaatttgtatccatattcagGGTTTTGTTGAAGATCAGTTTGGCTTAGGTTTGATTGCCAGAGCAGTTGAAGAAGGAATATCTGTCATCAAACCTGCAGGGATTATGATATTTAACATGG

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|29630290|gb|CB635299.1|CB635299
EST:     ATTCCAGTGAGGAGTTCTTGTATTCATTGAGTAACTACTGTGCTCTTCAG                         GGTTTTGTTGAGGACCAATTTGGCCTTGGGTTGATTGCTCGGGCTGTTGAA
genomic: ATTCCAGTGAGGAGTTCTTGTATTCATTGAGTAACTACTGTGCTCTTCAGgtaaactgaa ... ttgcatccagGGTTTTGTTGAGGACCAATTTGGCCTTGGGTTGATTGCTCGGGCTGTTGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaccccagtaatccactgcttgttatcttagtgcacaccttattgcatccagGGTTTTGTTGAGGACCAATTTGGCCTTGGGTTGATTGCTCGGGCTGTTGAAGAAGGGATATCAGTCATAAAGCCTATGGGTATTATGATATTTAACATGG
 ctttaac  putative branch site (score: 3)
                                        ccttatt  putative PPT
                         ttatctta  TA-rich tract