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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctttggacaatgattgatctgttgaatacatccacaaatagttttcagatttgcagaacctgtttttccgttttctgatggttatgaaaaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA

Basic information

species Oryza sativa
transcript LOC_Os03g09250.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 3
atctttggacaatgattgatctgttgaatacatccacaaatagttttcagatttgcagaacctgttttt----ccgttttctgatggttatgaaaaaaa------ttcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA
        ||| |  | |   | ||||  |      | ||  | || |||||| |||||  | || |||     | | || | |||   | |     ||      ||||||||||||| || ||| |||||||||| ||||||||||||||||||||||||||||| ||  | ||||||||||| ||||| || || ||||| |||||||
--------acactcgt-gcagtattgacgatggt-gctaactggttgcagattcgcagactcggtgtttgttatcttcttttcatgaccaagtgttgaactggttttcagGTGAACCCAGACGACATTGTGTTCGGAGGCTGGGACATTAGCAACATGAACCTGGCCGACTCCATGACCAGGGCCAAGGTGCTGGATATTGACCTGCAGA

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 1
atctttggacaat---gattgatctgttgaatacatccacaaatagttttcagatttgcagaacctgtttttccgttttctgatgg-ttatgaaaaaaatt--cagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA
     ||| || |   || ||| | || |     |         | |  ||| | ||       ||  |||||        | ||   |||  ||    ||  ||||||||| |||| ||||||||||| || ||||||||||| |||| ||||||| |||| ||||| ||||||||||| ||||| || |||||||| || ||||
-----tgggcagtactgactga-cggtggtgctaactggttgtaaatcctcaaacttttgaggtcttgttttcatgaccaagttgaactattgaactggttttcagGTGAACACTGACGACCTTGTGTTTGGAGGCTGGGACATCAGCATCATGAACTTGGCAGATGCCATGACCAGGGCCAAGGTGCTGGACATTGACCTACAGA

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 3
atctttggacaatgat--tgatctgttgaatacatccacaaatagttttcagatttgcagaacctgtttttccgttttctgatgg-ttatgaaaaaaatt--cagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA
     ||| || |  |      | || |     |         | |  ||| | ||       ||  |||||        | ||   |||  ||    ||  ||||||||||| || ||||||||||| || ||||||||||| |||| |||||||||||| ||||| ||||||||||| ||||| || |||||||| |||||||
-----tgggcagtactgacagacggtggtgctaactggttgtaaatcctcaaacttttgaggtcttgttttcatgaccaagttgaactattgaactggttttcagGTGAACCCAGACGACCTTGTGTTTGGAGGCTGGGACATCAGCAGCATGAACCTGGCAGATGCCATGACCAGGGCCAAGGTGCTGGACATTGACCTGCAGA

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G02210.1 (Glycine max), 3'ss of exon 3
-----------------------------------------atctttggacaatgattgatctgttgaatacatccacaaatagttttcagatttgcagaacctgtttttccgttttctgatggttatgaaaaaaatt------cagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA
                                         |  ||| | |   |     |   |||||    |  ||| ||        | | |    ||  | ||| |   ||  || ||||   ||||| ||||       ||||| || ||||| ||| ||||||| ||||| ||||| || ||||||||||||||||||||||| ||| |||||||||||||  ||||||| ||| ||||||
gtatcattacaacaatttatcattttttaattgattttatcagatttagtcctcggagtgttgattgaagtttttgacatatgcccacttgttgtagttaaggtttttgtaacttagcttatggccttgaaataaatctgttggcagGTTAATCCTGACGACATTGTGTTTGGGGGATGGGATATCAGCAACATGAACCTGGCTGATGCCATGGCCAGGGCAAAGGTGTTTGACATCGATTTGCAGA

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G31450.2 (Glycine max), 3'ss of exon 3
atctttggacaatgattgatctgttgaatacatccacaaatagttttcagatttgcagaacctgttttt----ccgttttctga---tggttatgaaaaaaatt---cagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA
      ||||| ||| |||  ||||||| ||||  |   ||   | | | |||      || |  ||||    || |    | |    |  | | ||  || ||   ||||| |||||||||||  ||||||| ||||| ||||| || || ||| |||||||||| ||||| ||| ||||||| |||||  |||| || || |||||||
------ggaca-tgagtgacatgttgaaaacatata---attactattaaattaattatacttactttttgaaccatgccataaacacgagtcttaattaatttatgcagGTAAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCAGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 2
--atctttggacaatgattgatctgttgaatacatccacaaatagttttcagatttgcagaacctgtttttccgttttctgatggttatgaaaaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA
  |  ||   ||| || |  |    |  ||| | |  |  ||   |  | || |||    | | ||   |          ||   |||   ||   || |||||||||||||||||  ||||||| ||||| ||||| || || ||| |||||||||||||||| ||| ||||||| |||||  |||| || || |||||||
ataatttctaaca-tgctgaaaacataaaattcttaaattaactatacttag-tttctgaaccatgccataattaaacacgagtcttaattaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 3
atctttggacaatgattga--tctgttgaatacatccacaaatagttttcagatttgcagaacctgtttttc-cgttttctgatggttatgaaaaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA
    |  |  | | | | |  |   ||||| | ||   ||  | ||    ||  ||     |  | ||| |    |  | | ||   ||| | ||  || ||||||||||| |||||| |||| || ||||| |||||||| ||  ||||||||||||| ||||| ||| ||||||| ||||| || ||||||||||||||||
---gtaagttagtaactcaatttcattgaaaatatttgcatgt-gtggaaagcattatttgatttatttatagtatgatataatttatattataatgat-cagGTGAACCCAGATGACATTGTTTTTGGGGGATGGGACATCAGTGACATGAACCTGGCAGATGCAATGGCCAGGGCTAAGGTCCTGGACATTGATCTGCAGA

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|29646112|gb|CB651119.1|CB651119
EST:     GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATG                         GTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
genomic: GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATGgtaatctgtc ... aaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
EST: gi|58598823|gb|CK009351.1|CK009351
EST:     GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATG                         GTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
genomic: GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATGgtaatctgtc ... aaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
EST: gi|58664958|gb|CK053644.1|CK053644
EST:     GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATG                         GTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
genomic: GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATGgtaatctgtc ... aaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
EST: gi|58609519|gb|CK037552.1|CK037552
EST:     GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATG                         GTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
genomic: GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATGgtaatctgtc ... aaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
EST: gi|13420717|gb|AU174807.1|AU174807
EST:     GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATG                         GTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
genomic: GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATGgtaatctgtc ... aaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
EST: gi|58606593|gb|CK034626.1|CK034626
EST:     GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATG                         GTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
genomic: GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATGgtaatctgtc ... aaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
EST: gi|58686865|gb|CK075552.1|CK075552
EST:     GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATG                         GTGAACCCTGATGA
genomic: GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATGgtaatctgtc ... aaaaattcagGTGAACCCTGATGA
EST: gi|58602603|gb|CK013131.1|CK013131
EST:     GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGGCCATG                         GTGAACCCTGA
genomic: GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATGgtaatctgtc ... aaaaattcagGTGAACCCTGA
EST: gi|29616445|gb|CB621457.1|CB621457
EST:     GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATG                         GTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC
genomic: GCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATGgtaatctgtc ... aaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAAC

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: 75 (upstream exon), 73 (downstream exon)
Score: 164

AGCCAACTACTATGGCTCACTCACCCAGGCGTCCACCATCAGGGTCGGGAGCTACAACGGGGAGGAGATCTACGCGCCCTTCAAGAGCCTCCTGCCCATGgtaatctgtc ... aaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagatttgcagaacctgtttttccgttttctgatggttatgaaaaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA
                             ttctgat  putative branch site (score: 164)
                                      ttatgaaaaaaattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctttggacaatgattgatctgttgaatacatccacaaatagttttcagatttgcagaacctgtttttccgttttctgatggttatgaaaaaaattcagGTGAACCCTGATGACCTTGTGTTCGGGGGCTGGGACATTAGCAACATGAACCTGGCTGATGCTATGACCAGGGCAAAGGTACTTGACATTGATCTGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG