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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcatcctacataatatttcattattcaatgtacgggttttgaggacatctgttctaaactacttggcgacattacattcccatatcctgtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os09g10600.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 10
-ttgcatcctacataatatttcattattcaatgtacgggttttgaggacatctgttctaaactacttggcgacattacattcccatatcctgtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG-
  ||||   ||  |  |   |      |  || |  |  | |  | || ||    |  ||| |  |   | |  ||   ||    | |  |   |    ||||||||||||||| || ||||| ||||| ||||||||||| || | |||||| || ||||| |     || |||||||||||||| || ||    || | 
agtgcaagttaactctttccttcaagatggatttttgcatgtcaatga-attcagtagaaattgataaac-atgttgacttgaattgttttcaatggctaggTCCATTGGGAAGCCGTGCAGCGAAAGCGATTGGTTTCATTGACATGATGATTGACTATTCATTTACCAATGCACCACTGCAGAAAGAACTACATGCTGG

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G45990.1 (Glycine max), 3'ss of exon 11
ttgcatcctacataatatttcattattcaatgtacgggttttgaggaca-tctgttctaaactacttggcgacattacattcccatatcctgtt---tctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG
    || | |  |||   ||  |  ||||| |||    |||  | | || |   |||   || | |||   |         |    || || ||   |    ||||||||||||||| || ||||| ||||| ||||| ||||| || | |||||| || |||||||     || |||||||||||||| || ||    || |
--aaatgcaagttaactctt--tccttcaaggtagatttttgcatgtcagtgaattcagtacaaattgataaacacgttgacttgaattcttttcaatggctagGTCCATTGGGAAGCCGTGCAGCAAAAGCAATTGGCTTCATTGACATGATGATTGACTATTCGTTTACCAATGCACCACTGCAGAAAGAACTACATGCTG
















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|86505190|gb|CI147823.1|CI147823
EST:     TTACGAAGCAGCTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAG                         GTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
genomic: TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAGgtatcttaca ... gtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
EST: gi|33693872|gb|CF322111.1|CF322111
EST:     TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAG                         GTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
genomic: TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAGgtatcttaca ... gtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
EST: gi|29640102|gb|CB645111.1|CB645111
EST:     TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAG                         GTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
genomic: TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAGgtatcttaca ... gtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
EST: gi|87027842|gb|CI276198.1|CI276198
EST:     TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAG                         GTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
genomic: TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAGgtatcttaca ... gtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
EST: gi|58669339|gb|CK058025.1|CK058025
EST:     TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAG                         GTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
genomic: TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAGgtatcttaca ... gtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
EST: gi|29670467|gb|CB666742.1|CB666742
EST:     TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAG                         GTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
genomic: TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAGgtatcttaca ... gtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
EST: gi|218501539|gb|FG956143.1|FG956143
EST:     TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAG                         GTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
genomic: TTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAGgtatcttaca ... gtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
EST: gi|88902832|gb|CI088370.1|CI088370
EST:     CATATCAGCAG                         GTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA
genomic: CATATCAGCAGgtatcttaca ... gtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGA

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), 71 (downstream exon)
Score: 25

GTTCTAGCTTACGAAGCAGGTCGAAAAGGCAAGATCAGAGTGAATACCATATCAGCAGgtatcttaca ... gtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacatctgttctaaactacttggcgacattacattcccatatcctgtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG
        ttctaaa  putative branch site (score: 25)
                                         tcctgtttct  putative PPT
                           attacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcatcctacataatatttcattattcaatgtacgggttttgaggacatctgttctaaactacttggcgacattacattcccatatcctgtttctgcagGTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
-tgcatcc
- - - - - - - - -tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattccc