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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaagtgttatgaatttttcatggtatagtgcccaacttccattggaaccatgctaagctttttgtaactgattcacagGTGGCTGCAATATTTAAAATTGGCAACAGCAAAGACATACCCGATATTCCAGATCATCTTTCTTTTGAGGCAAAGAACTTTTTGAAACTTTGCTTGCAGC

Basic information

species Oryza sativa
transcript LOC_Os11g10100.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA05G32510.1 (Glycine max), 3'ss of exon 8
----gtaagcaagtgtt-----atgaatttttcatggtatagtgcccaact--tccattggaaccatgctaagc-tttttgtaactgattca-cagGTGGCTGCAATATTTAAAATTGGCAACAGCAAAGACATACCCGATATTCCAGATCATCTTTCTTTTGAGGCAAAGAACTTTTTGAAACTTTGCTTGCAGC
    |  |     |  |     |  |  ||||  | | |||   ||    |  |  ||  |||  |    ||   ||||| |    |||| | ||||| ||||| |||||||||||||| ||||||||||| || || || || || || ||||||||    || ||||| || ||  | || || ||||| ||  
gtgagatattggatacttcagaactagcttttacttgcataac-cctgtttggtgaatatgaatgactaaaattgtttttatgttggattgaacagGTAGCTGCCATATTTAAAATTGGGAACAGCAAAGATATGCCTGAAATCCCCGAGCATCTTTCGAACGATGCAAAAAATTTCATCAAGCTATGCTTACAAA

upper sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G15870.1 (Glycine max), 3'ss of exon 9
---------------------gtaagcaagtgttatgaatttttcatggtatagtgcccaacttccatt--ggaaccatgctaagctttttgtaactg-attcac-agGTGGCTGCAATATTTAAAATTGGCAACAGCAAAGACATACCCGATATTCCAGATCATCTTTCTTTTGAGGCAAAGAACTTTTTGAAACTTTGCTTGCAGC
                        |||| || || || || |||  | | |   |     |     ||   ||| | |   |    |||   |  ||| |||||| |||| |||||||||||||||||||| ||||||| ||| || || || ||||| ||||| || ||   |||||||||||| ||  |  | || ||||| ||  
gtatgattttggatatttagaactagcatgtatt-tgcatatttgctaggagcctatttgaagagtatgaaggaccaacattgttttttcaatgcctgtattcaccagGTAGCTGCAATATTTAAAATTGGTAACAGCAGAGATATGCCTGAAATTCCGGATCACCTCTCAAGTGAGGCAAAGAATTTCATTCAGCTATGCTTACAAA

upper sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA04G39110.1 (Glycine max), 3'ss of exon 8
---------------------gtaagcaagtgtt-atgaatttttcatggtatagtgcccaacttccattggaaccatgctaagctttttgtaactg-attca-cagGTGGCTGCAATATTTAAAATTGGCAACAGCAAAGACATACCCGATATTCCAGATCATCTTTCTTTTGAGGCAAAGAACTTTTTGAAACTTTGCTTGCAGC
                        |||| || ||     ||||   |||      |    |   |      |  | |   |    ||||  |  ||| ||||| ||||| |||||||||||||||||||| ||||||| ||| || || || ||||| |||||||| ||    ||||||||||| ||  |  | || ||||| ||  
gtatgattttggatatttagaactagcatgtatttgcatatttgctatgagcctattttaagagtatgaaaggccaacattgtttttttaatgcctgtattcaacagGTAGCTGCAATATTTAAAATTGGTAACAGCAGAGATATGCCTGAAATTCCTGATCATCTCTCAAGCGAGGCAAAGAAATTCATTCAGCTATGCTTACAAA

upper sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G16670.1 (Glycine max), 3'ss of exon 8
----gtaagcaagtgtt-----atgaatttttcatggtatagtgcccaacttccattggaaccatgctaagct--ttttgtaactgattca-cagGTGGCTGCAATATTTAAAATTGGCAACAGCAAAGACATACCCGATATTCCAGATCATCTTTCTTTTGAGGCAAAGAACTTTTTGAAACTTTGCTTGCAGC
    |  |     |  |     |  |  ||||  | |||||   |         | |   |     | ||  |  |||| |    || | | ||||| ||||| |||||||||||||| ||||||||||| || || || || || || ||||||||   ||| ||||| || ||  | || || ||||| ||  
gtgagatattggatacttcagaactagcttttacttgtataaccctgtttggtgaatatgaatgaccaaaattgtttttatgttggactgaacagGTAGCTGCCATATTTAAAATTGGGAACAGCAAAGATATGCCTGAAATCCCCGAGCATCTTTCGAATGATGCAAAAAAATTCATCAAGCTATGCTTACAAA

upper sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------gtaagcaagtgttatgaatttt-tcatggtatagtgcccaacttccattggaaccatgctaagctttttgtaactgat-tcacagGTGGCTGCAATATTTAAAATTGGCAACAGCAAAGACATACCCGATATTCCAGATCATCTTTCTTTTGAGGCAAAGAACTTTTTGAAACTTTGCTTGCAGC
                        ||    |  ||  | | |||| | | |||   |||   ||  | | |    ||||  | |   || |  |     || | ||||||||||||||| ||||||||||| |||||||  ||  | || || ||||| ||||| ||||||  ||| ||||| |  ||| | |  || |||||||| |
gtgagattgtggatatttgggccatattttatagtagttatttttgttaaggtcaggtgtgaaatgttcgt--agaccaaaccat-tttatcatgttgaatgtgacagGTGGCTGCAATTTTTAAAATTGGAAACAGCAGGGATGTCCCTGAAATTCCCGATCACCTTTCTAATGATGCAAAAAGTTTTGTAAGGCTATGCTTGCAAC

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|109974299|gb|DT806830.1|DT806830
EST:     CCATTATTGAGATGGGAACCGCAAGACCTTCTTGGATTCAGTATGAAGGG                         GTGGCTGCAATATTTAAAATTGGCAACAG
genomic: CCATTATTGAGATGGCAACCGCAAGACCTCCTTGGATTCAGTATGAAGGGgtaagcaagt ... tgattcacagGTGGCTGCAATATTTAAAATTGGCAACAG
EST: gi|29680776|gb|CB677051.1|CB677051
EST:     CCATTATTGAGATGGCAACCGCAAGACCTCCTTGGATTCAGTATGAAGGG                         GTGGCTGCAATATTTAAAATTGGCAACAGCAAAGACATACCCGATATTCCA
genomic: CCATTATTGAGATGGCAACCGCAAGACCTCCTTGGATTCAGTATGAAGGGgtaagcaagt ... tgattcacagGTGGCTGCAATATTTAAAATTGGCAACAGCAAAGACATACCCGATATTCCA
EST: gi|58594079|gb|CF992387.1|CF992387
EST:     CCATGATTGAGATGGCAACCGCAAGACCTCCTTGGATTCAGTATGAAGGG                         GTGGCTGCAATATTTAAAATTGGCAACAGCAAAGACATACCCGATATTCCA
genomic: CCATTATTGAGATGGCAACCGCAAGACCTCCTTGGATTCAGTATGAAGGGgtaagcaagt ... tgattcacagGTGGCTGCAATATTTAAAATTGGCAACAGCAAAGACATACCCGATATTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagtgcccaacttccattggaaccatgctaagctttttgtaactgattcacagGTGGCTGCAATATTTAAAATTGGCAACAGCAAAGACATACCCGATATTCCAGATCATCTTTCTTTTGAGGCAAAGAACTTTTTGAAACTTTGCTTGCAGC
                                   tttttgtaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaagtgttatgaatttttcatggtatagtgcccaacttccattggaaccatgctaagctttttgtaactgattcacagGTGGCTGCAATATTTAAAATTGGCAACAGCAAAGACATACCCGATATTCCAGATCATCTTTCTTTTGAGGCAAAGAACTTTTTGAAACTTTGCTTGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC