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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaaacttctaaattcttattgctagctcgttctgattctttcaaagattttgctgatatggagtgacatattggaatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA

Basic information

species Oryza sativa
transcript LOC_Os05g38370.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G035922_T02 (Zea mays), 3'ss of exon 2
gtataaaacttctaaattcttattgctagctcgttctgattctttcaaagattttgc-tgatatggagtgacatatt-ggaatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA
          | | ||   ||    ||  |||| | ||   ||||||     | ||  ||| ||||  || |||||    || | | |||||||| || ||||||||||| ||||||||  ||||||| ||||| |||  |||||| || || |||||||| || || ||
-------gtatgtcaacgtttgcgtct--ctcgctttggc-ctttcaccatctctgtgtgacatggtctggcatatccaaaaaaattaagGTTGGCGAGGTTGCAAAAATTACATGCAAATCAGAATATGCATATGGAGCTGCAGGCTCACCACCAGAGATACCTCCTAA

upper sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G04170.1 (Glycine max), 3'ss of exon 3
--gtataaaacttctaaattcttattgctagctcgttctgattctttcaaagattttgctgatatggagtgacatattg--gaatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA-
      || | |   |||      ||   |      | |  ||   | |  | ||||  |  |||    ||      ||   | | |   ||||||| ||||||||||||||||| |||||||||||||| ||||| || |||||||| || || ||||| ||||| ||  | 
tctagcaatagtaacaaagcaaacttttgatgaaactatatttgaataagggtttttaattttatctcatgcttatctgctaattttcccaggTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAG

upper sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G34120.1 (Glycine max), 3'ss of exon 3
gtataaaacttctaaattcttattgctagctcgttctgattctttcaaagattttgctgatatggagtgac-atattggaatattga-agGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA
|| ||| |   | ||| | ||  ||  |     ||   ||      || | |||   |  | |    ||   || |   ||| |||  ||||||| ||||||||||||||||| |||||||||||||| ||||| || |||||||| || || ||||| ||||| ||  |
gtctaacaaagc-aaacttttgatgaaactatatttaaata-----aaggttttcaattttttctcatgcttatctgctaattttgccagGTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGA

upper sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G55520.1 (Arabidopsis thaliana), 3'ss of exon 3
gtataaaacttcta-aattcttattgctagctc-gttctgattctttcaaagattttgctgatatggagtgacatattggaatatt---gaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA
         ||||| |||| | | |  |   ||  | || ||  | | || | ||  | |  |||  |   ||  ||| || | ||     ||||||| |||||||||||||| ||||| ||||||||||| || |||||||| || ||||| || || || || |||||  |
-------gtttctacaattttgagtctttcttctatccttataatctgaacgcttcagttattatata-caactgatttgattttttttacagGTTGGAGAAGTTGCAAAAATTACATGTAAGCCAGAATATGCTTACGGAAGAGCCGGGTCTCCTCCCGACATCCCACCTGA

upper sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 3
---gtataaaacttctaaattcttattgctagctcgtt-ctgattct--ttcaaagattttgctgatatggagtgacatattggaatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA
        |  |||  |  ||  | |||| |  || || ||| ||    || |||| |  || | | |||   |   || |||   | ||  ||||||| || ||||||||||| || ||||||||||| ||||||||||||  ||| || || || ||||| || ||  |  |
gttaatctattcttacagctttatcttgccatatcttttctggttaaagttgaaagttcctgtt-acatgttcttttatgttgtt-tcttccagGTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA

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|58653405|gb|CK042085.1|CK042085
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGT
EST: gi|25044727|gb|AJ420710.1|AJ420710
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|88209738|gb|CI209587.1|CI209587
EST:     GAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|14571477|gb|BI118845.1|BI118845
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAA-TAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|88836064|gb|CI371169.1|CI371169
EST:     GCCAAGGAGCTCTCATTAAAGCAT-GGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACCCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|38477260|gb|CF961393.1|CF961393
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|58670906|gb|CK059592.1|CK059592
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|58676992|gb|CK065679.1|CK065679
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|88980703|gb|CI022414.1|CI022414
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|88572905|gb|CI664476.1|CI664476
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGC
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgattctttcaaagattttgctgatatggagtgacatattggaatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA
                     tgctgat  putative branch site (score: 3)
             aaagatttt  TA-rich tract