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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaatgactgaataagacaactcacctgacccctcatggttgatgctccagcatgcaaactttcatcattgattcactgtgctcctttcaactttgaaaaaacaaattactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTA

Basic information

species Oryza sativa
transcript LOC_Os08g14460.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G147500_T02 (Zea mays), 3'ss of exon 11
gtagaa-tgactgaat-aagacaactcacctgacccctcatggttgatgctccagcatgcaaactt-tcatcattgattcactgtgctcctttcaactttgaaaaaacaaattactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTA
|||| |   |||| ||  |||| |    | |  |     || | |  | ||||  ||| || |||| |  |||||   | |   |  |  ||||     |||          |   |  ||||| ||||||||||||||||||||||| || || |||||||||||||| || || || || || ||||| ||||| |||||||||||||| |||||||| |
gtaggagccactggattgagactataagcat--cgtacaattgctatttctcc--catacacacttgttttcattacatgatgataattatttc-----tga----------tgacaaccagGCACGAATGACACAACTTCAAGATGCTCAGAAAGGTGCAGAAGTGACTTCTGAGGCAACTGACCGGGAGCTTGAGCTTGAAGCTCAACTGGTTGAAGCAA

upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA17G07040.1 (Glycine max), 3'ss of exon 12
gtagaatgactgaataagacaactcacctgacccctcatggttgatgctccagcatgcaaact-ttcatcattgattcactgtgctcctttcaactttgaaaaaacaaattactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTA
    ||| ||| | ||  |  |||  ||          |  |   |  |     ||   |||| ||  || ||| ||             | ||||     ||||   |  | |||| |||  || |||   ||| | |||||||| ||||| |  |||||||| || ||||| ||||| ||| |||||||||| |||||||||||||| || ||||| |
--gtaattacttattagtatcactttccaatttgtatcttttaagtatttgcagatatgaactgtttgtctttggttg------------ttaactgcttgaaaattga--aatatgaagGAGCGTATGGTTCAATTGCAAGATGCTCAAAAAGAAGCAGAAGTTACTTCAGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA

upper sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 12
gtagaatgactgaataagacaactcacctgacccctcatggttgatgctccagcatgcaaactttcatcattgattcactgtgctcctttcaactttgaaaaaacaaattactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTA
    ||| ||| | ||  |  |||  ||  |    | ||  || | |     ||||  |    |  |   ||||||  || || |  ||      |||||||   ||||    ||| |||  || |||   ||| | |||||||| |||||||  |||||||| || || || ||||| ||| |||||||||| |||||||||||||| || ||||| |
--gtaattacttattagtatcactttcc--aatttttatcttttaagtatttgcatatatgaatgaa---ttgattgtctttggttgttaactgcttgaaaattgaaat----atgaagGAGCGCATGGTTCAATTGCAAGATGCTCAAAAGGAAGCAGAAGTTACTTCTGAGGCTACTGAGAGGGAACTTGAGCTTGAAGCTCAACTTGTCGAAGCAA

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|27921121|gb|CB096929.1|CB096929
EST:     CTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAG                         GCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
genomic: CTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAGgtagaatgac ... tactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
EST: gi|38479439|gb|CF963558.1|CF963558
EST:     CTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAG                         GCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
genomic: CTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAGgtagaatgac ... tactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
EST: gi|163929464|gb|EG713433.1|EG713433
EST:     GAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAG                         GCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
genomic: GAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAGgtagaatgac ... tactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
EST: gi|88847034|gb|CI001306.1|CI001306
EST:     AGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAG                         GCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
genomic: AGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAGgtagaatgac ... tactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
EST: gi|58686401|gb|CK075088.1|CK075088
EST:     CTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAG                         GCCCGCATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
genomic: CTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAGgtagaatgac ... tactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
EST: gi|27920604|gb|CB096412.1|CB096412
EST:     CTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAG                         GCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
genomic: CTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAGgtagaatgac ... tactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
EST: gi|58684457|gb|CK073144.1|CK073144
EST:     CTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAG                         GCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
genomic: CTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAGgtagaatgac ... tactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
EST: gi|86423209|gb|CI060782.1|CI060782
EST:     AGAGAGTTTGCGCACTAAAATGGCTTCCATAAAG                         GCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA
genomic: AGAGAGTTTGCGCACTAAAATGGCTTCCATAAAGgtagaatgac ... tactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 58 (upstream exon), 65 (downstream exon)
Score: 13

GATGTCTTTGATTTGCCCTTTCACATGGCTAGAGACCAGATTGAAGAGAGTTTGCGCACTAAAATGGCTTCCATAAAGgtagaatgac ... tactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcattgattcactgtgctcctttcaactttgaaaaaacaaattactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTA
    cattgat  putative branch site (score: 13)
                              tttgaaaaaacaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaatgactgaataagacaactcacctgacccctcatggttgatgctccagcatgcaaactttcatcattgattcactgtgctcctttcaactttgaaaaaacaaattactatgcagGCCCGAATGACACAACTTCAAGATGCCCAAAAGGGTGCAGAAGTGACATCAGAAGCTACCGAGCGGGAACTTGAACTTGAAGCTCAACTAGTTGAAGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC