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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcttctctatgctagtgaaactttgtttgcctaatatttttatgttccttcactttaaaatatccaatttttttttaacaccactttcttctcaacagGTGGTCAAACAAGCATCAG

Basic information

species Oryza sativa
transcript LOC_Os08g15040.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 5
-----------------------ctgcttctcta-tgctagtgaaactttgtttgcctaatatttttatgttccttcactttaaaatatccaattttt--ttttaacacca-ctttcttctcaacagGTGGTCAAACAAGCATCAG
                         |    | || | || ||  || |          |  |    ||   |  |       |  ||||  || |||   | ||||||||| |||||||||| |||||||||||||||||||||||
atgttttttgcattgtatagctgtagtgcgtatactacttgttcaattgcaaaaaaaaatcacagctaaagttttcagtgccatcatattaaactttcagTATTAACACCAACTTTCTTCTCGACAGGTGGTCAAACAAGCATCAG

upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G147726_T03 (Zea mays), 3'ss of exon 1
-------ctgctt-ctctatgctagtgaaactttgtttgcctaatatttttatgttccttcactttaaaatatccaatttttttttaacacca-ctttcttctcaacagGTGGTCAAACAAGCATCAG
       || |||  || ||   |   |||  |       ||||  |||| | || || |||  ||||| | ||        | ||||||||| |||||||||| |||||||||||||||||||||||
gcgtatactacttgttcaattgcaaaaaaaaatca--cagctaaagttttca-gtgccatcatattaaactttcag------tattaacaccaactttcttctcgacagGTGGTCAAACAAGCATCAG

upper sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G147726_T05 (Zea mays), 3'ss of exon 2
-------ctgctt-ctctatgctagtgaaactttgtttgcctaatatttttatgttccttcactttaaaatatccaatttttttttaacacca-ctttcttctcaacagGTGGTCAAACAAGCATCAG---------------------------------------------------------------------------------
       || |||  || ||   |   |||  |       ||||  |||| | || || |||  ||||| | ||        | ||||||||| |||||||||| |||||||||||||||||||||||                                                                                 
gcgtatactacttgttcaattgcaaaaaaaaatca--cagctaaagttttca-gtgccatcatattaaactttcag------tattaacaccaactttcttctcgacagGTGGTCAAACAAGCATCAGGTACCGGCTCTTTATCATGATAGTAAATTCCTGACTGTCATTTCTGAAGTAAATAATACTATTGCATTTATTTAATCACCG

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|88383993|gb|CI631883.1|CI631883
EST:     CGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG                         GTGGTCAAACAAGCATCAG
genomic: CGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCGgtgagtgtgc ... ttctcaacagGTGGTCAAACAAGCATCAG
EST: gi|27554607|gb|CA998507.1|CA998507
EST:     TGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG                         GTGGTCAAACAAGCATCAA
genomic: TGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCGgtgagtgtgc ... ttctcaacagGTGGTCAAACAAGCATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttccttcactttaaaatatccaatttttttttaacaccactttcttctcaacagGTGGTCAAACAAGCATCAG
                             ttttaac  putative branch site (score: 2)
                                   caccactttcttctc  CT-rich tract
     ttcactttaaaatatc  TA-rich tract