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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcactttgttacacatagaccttggttggctagaaattagtccctttttcacaaacatactgactgtagtttctttaaaatgttcatacatattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCTAAATGCCTTTACGATGCAATATCAAGACTGGAAAAGGC

Basic information

species Oryza sativa
transcript LOC_Os12g07190.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G126656_T01 (Zea mays), 3'ss of exon 3
tttcactttgttacacatagaccttggttgg----ctagaaattagtccctttttcacaaacatactgactgtagtttctttaaaatgttcatacatattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCTAAATGCCTTTACGATGCAATATCAAGACTGGAAAAGGC
   |  |||||| | ||| | ||||| || |    |  ||    ||||    ||  | |     ||| ||   || || |  || ||||||   ||||||||||| |||||||||||||| || ||||| ||||||||||||||||||||||||||||||||||| ||||||||||| || |||||| ||||||||||||||||
--gctgtttgtt-ctcat-gtccttgcttagaaaccctgagtcaagtcttagttggatatgttcactaacatcagcttttacaatatgttctctcatattttagGGAAATTTAGACACCTTCCCGTTGTAGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCAAAATGCCTTTATGAAGCAATAGCAAGACTGGAAAAGGC

upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G32930.1 (Glycine max), 3'ss of exon 3
--tttcactttgttacacatagaccttggttggctagaaattagtccctttttcaca-aacatactgactgtagtttctttaaaatgttcatacatattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCTAAATGCCTTTACGATGCAATATCAAGACTGGAAAAGGC
  ||||  || | | |     |       || |    || | || |  | | | | | ||   | | | ||   | |  || |    ||   ||  ||   ||||||||| || |||||||| ||||||||||||||||| || ||||| || ||||| ||| | | ||| ||||| ||||| ||| | ||  |||| |||||
tttttctattagattctgtctgtttacattttgtactaattgagacagtctataaaataatgcattaaatgagatatggtttattctttttaactgat---agGTAAATTCAGGCACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATACTGGATATTACCAGATGTCTTTATGATGCCATAACTAGGATGGAGAAGGC

upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G00560.2 (Glycine max), 3'ss of exon 3
tttcactttgttacacatagacc-ttggttggctagaaattagtccctttttcacaaacatactgactgtagtttctttaaaatgttcatacatattt-tagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCTAAATGCCTTTACGATGCAATATCAAGACTGGAAAAGGC
| ||  | | ||| |    | |  ||   |   ||| ||||    |  | |  | |||   |   | |  |     | | |  | |||||    | |  |||||||||| || |||||||| ||||||||||||||||| || ||||| || ||||| ||  | | ||| ||||| ||||| ||| | ||  |||| | |||
tatctttctattagattctgtctgtttactttgtagtaattgagacagtct--ataaagtaatccattaaatgagatatgatttattcattttaactgatagGTAAATTCAGGCACCTCCCTGTTGTGGAAAATGGTGAAGTGATTGCCATACTGGATATCACCAGATGTCTTTATGATGCCATAACTAGGATGGAGAGGGC

upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G16570.2 (Glycine max), 3'ss of exon 3
--tttcactttgttacacatagaccttggttggctagaaattagtccctttttcaca-aacatactgactgtagtttctttaaaatgttcatacatattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCTAAATGCCTTTACGATGCAATATCAAGACTGGAAAAGGC
   ||| || | ||    ||| | |||| |||     |   |||||    |   |   ||   | | | ||     | |     |  ||  |  |  |  |||||| ||||||||||||||| ||||||||||||||||| || ||||| |||||||| ||  | ||||| ||||| ||||| ||||| ||| |||| |  ||
ggattctctatttt---tatacatcttgtttgatagaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC

upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G38480.1 (Glycine max), 3'ss of exon 3
-tttcactttgttacacatagaccttggttggctagaaattagtccctttttca-caaacatactgactgtagtttctttaaaatgttcatacatattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCTAAATGCCTTTACGATGCAATATCAAGACTGGAAAAGGC
  ||   ||   |    ||| | |||| ||          |||||    |   | | ||   | | | ||     | |  ||  ||    |  |  |  |||||||||| ||||||||||| || |||||||||||||| || ||||| |||||||| ||| | ||||||||||| ||||| ||||| ||  |||| |  ||
tattagattctctgtttatacatcttgtttaatagagtcatagtcggactggaaactaattcattaagtgagagatat--aatttgactttttaactgatagGTAAATTCAGACACCTCCCTGTCGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATTACCAAATGCCTTTATGATGCCATATCTAGGATGGAGAGCGC

upper sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv07s0031g02750.t01 (Vitis vinifera), 3'ss of exon 3
-tttcactttgttacacatagac-cttggttggctagaaattagtccctttttcacaaacatactgactgtagtttctttaaaatgttcatacatattt-tagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCTAAATGCCTTTACGATGCAATATCAAGACTGGAAAAGGC
  || | ||  || || |||  | |||  || |   ||| |   |   ||  | |  | | || |   |||  ||     |   || |  |     |    ||| || ||||| |||||||| ||||| ||||||||||| |||||||| ||  |||| ||| | || ||||| || ||||| |||||  || |||| |||||
tatttatttcatttcatatatgcacttcatttgaatgaattc--tttattacttattagcctaatatttgtt-ttatggcatcttgcttgtgttggtcaacagGCAAGTTTAGGCACCTCCCTGTTGTAGAAAATGGTGAAGTTATTGCCATATTGGATATTACAAAGTGCCTCTATGATGCTATATCTCGAATGGAGAAGGC

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|29628514|gb|CB633525.1|CB633525
EST:     TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAG                         GTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
genomic: TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAGgtatgtcaga ... catattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
EST: gi|29616351|gb|CB621363.1|CB621363
EST:     TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAG                         GTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
genomic: TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAGgtatgtcaga ... catattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
EST: gi|58605735|gb|CK033768.1|CK033768
EST:     TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAG                         GTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
genomic: TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAGgtatgtcaga ... catattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
EST: gi|29620736|gb|CB625747.1|CB625747
EST:     TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAG                         GTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
genomic: TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAGgtatgtcaga ... catattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
EST: gi|29683887|gb|CB680162.1|CB680162
EST:     TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAG                         GTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
genomic: TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAGgtatgtcaga ... catattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
EST: gi|38475232|gb|CF959365.1|CF959365
EST:     TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAG                         GTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
genomic: TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAGgtatgtcaga ... catattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
EST: gi|58663826|gb|CK052512.1|CK052512
EST:     TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAG                         GTAAATTTAGACACCTCCCAGTTGTGGAACATGGTGAGGTTATTGCTATGC
genomic: TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAGgtatgtcaga ... catattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
EST: gi|58693946|gb|CK082633.1|CK082633
EST:     TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAG                         GTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
genomic: TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAGgtatgtcaga ... catattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
EST: gi|29617498|gb|CB622510.1|CB622510
EST:     TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAG                         GTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC
genomic: TGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAGgtatgtcaga ... catattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGC

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: 72 (upstream exon), 71 (downstream exon)
Score: 34

CGGGTGGAGCAAACCATCATGTCCAAGATCATGACAAGGAACCCCACATATGCCATGTCTGATACGCTTGCCATTGAAGCATTGCAGAAGATGGTTCAAGgtatgtcaga ... catattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCTAAATGCCTTTACGATGCAATATCAAGACTGGAAAAGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttcacaaacatactgactgtagtttctttaaaatgttcatacatattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCTAAATGCCTTTACGATGCAATATCAAGACTGGAAAAGGC
              tactgac  putative branch site (score: 34)
                          tttctttaaaatgttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcactttgttacacatagaccttggttggctagaaattagtccctttttcacaaacatactgactgtagtttctttaaaatgttcatacatattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCTAAATGCCTTTACGATGCAATATCAAGACTGGAAAAGGC

- - - - - - acacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgactg