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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttaatccactggctcctgcataaacaaaacattctaatagctactggtgcaattagaattagcagctattggtgcttaatatgtatcacaatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGCATTCCATGACAGCAAGCTGCTGATGGAGACCTGCCAGGAGGCCAAGAAT

Basic information

species Oryza sativa
transcript LOC_Os01g23680.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G022090_T02 (Zea mays), 3'ss of exon 3
-ccttaatccactggctcctgcataaacaaaacattctaatagctactggtgcaattagaattagcagctattggtgct-taatatgtatcacaatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGCATTCCATGACAGCAAGCTGCTGATGGAGACCTGCCAGGAGGCCAAGAAT
   || |   |  |  ||     ||     | |  | || ||     |  ||  | |||||| | || || |   |    |   |  | |  |||| |||||||||||||| |||||||||||||| ||||||||||||||||| || || || |||||||||||||||||||||||||| || ||||||||||||||||| 
ggattgaaagag-gagtcacatttatttttatctctgtattaatatgtattgtgactagaat-accacctttatatctagtggcaactgttgcaatcttcagGTTATGCAATATGGACATCATCTCCAAGGTCCAACAGGTGATCTGCTTCGCGTTCCATGACAGCAAGCTGCTGATGGAAACATGCCAGGAGGCCAAGAAC

upper sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 5
ccttaatccactggctcctgcataaacaaaacattctaatagctactggtgcaattagaattagcagctattggtgcttaatatgta---tcacaatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGCATTCCATGACAGCAAGCTGCTGATGGAGACCTGCCAGGAGGCCAAGAAT
  |  |   |  |       |||   |     ||    | |  ||   ||    | |  || |       ||  ||||||||   ||   |  ||||   |||||||||||| |||||||||||||| |||||||||||||| || || || || ||||| |||||||| ||||||||||| || ||||||||||||| ||| 
--tggactgaaagagagtcacattt-ctttttatctgtacatatatatgtattgtgactataatatcacctttatgcttaatggctactgttgcaatcaccagGTTATGCAATATGGACATCATCTCTAAGGTCCAACAGGTAATCTGCTTCGCGTTCCACGACAGCAAACTGCTGATGGAAACATGCCAGGAGGCCATGAAC

upper sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv10s0042g00120.t01 (Vitis vinifera), 3'ss of exon 4
--ccttaatccactggctcctgc-ataaacaaaacattctaatagctactggtgcaattagaattagcagctattggtgcttaatatgtatcacaatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGCATTCCATGACAGCAAGCTGCTGATGGAGACCTGCCAGGAGGCCAAGAAT
   |  | | | | |   | | |  ||    |||   | |  | | ||    |||||  || | |   | ||  |  |  ||  | | |   | |   | |||||| || ||| | ||||||||  |    || || || || ||||| ||||| ||||||||||||||| |||||||||| || || || |||||||  || 
tgtcagacttctcagtagcattctgtactttaaattattttctgggta--aatgcaaagaggactc-tatctgatcattgttcttgtcttggagagactgcagGTTGTGTAACCTTGACATCATTACTTGTGTACAGCAAGTCATTTGCTTTGCCTTCCATGACAGCAAGTTGCTGATGGAAACATGTCAAGAGGCCAGAAAC

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|88486774|gb|CI424045.1|CI424045
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|88489982|gb|CI427254.1|CI427254
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|88476720|gb|CI413991.1|CI413991
EST:     GCCTCAATATGACCATTTGCCACTAATTGAAGGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTG
genomic: GCCTCAATATGACCATTTGCCACTAATTGAA-GCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTG
EST: gi|86600917|gb|CI356674.1|CI356674
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|29659908|gb|CB656183.1|CB656183
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|29658365|gb|CB654640.1|CB654640
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|86840964|gb|CI335120.1|CI335120
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|88466708|gb|CI542285.1|CI542285
EST:     TTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|86822200|gb|CI357833.1|CI357833
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|88487063|gb|CI424334.1|CI424334
EST:     CATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: CATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|163923267|gb|EG711076.1|EG711076
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATC
EST: gi|18386357|gb|BM419555.1|BM419555
EST:     TAATTGAGAACGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TAATTGAGAA-GCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|88448408|gb|CI555263.1|CI555263
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|88461056|gb|CI550219.1|CI550219
EST:     ACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: ACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|88368453|gb|CI561527.1|CI561527
EST:     GACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: GACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|29657705|gb|CB653980.1|CB653980
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|88441092|gb|CI538788.1|CI538788
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|29660019|gb|CB656294.1|CB656294
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|25807329|gb|CA763290.1|CA763290
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|86903462|gb|CI322945.1|CI322945
EST:     TAA-TGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCACG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTG
genomic: TAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCA-Ggtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTG
EST: gi|86500098|gb|CI142731.1|CI142731
EST:     TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: TTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
EST: gi|88456963|gb|CI529164.1|CI529164
EST:     GAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG                         GTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC
genomic: GAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGC

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: 55 (upstream exon), 73 (downstream exon)
Score: 7

GTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAGgtatgtcagc ... caatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGCATTCCATGACAGCAAGCTGCTGATGGAGACCTGCCAGGAGGCCAAGAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtgcaattagaattagcagctattggtgcttaatatgtatcacaatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGCATTCCATGACAGCAAGCTGCTGATGGAGACCTGCCAGGAGGCCAAGAAT
                              gcttaat  putative branch site (score: 7)
       aattagaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttaatccactggctcctgcataaacaaaacattctaatagctactggtgcaattagaattagcagctattggtgcttaatatgtatcacaatattcagGTTATGCAACATGGACATCATCTCGAAGGTCCAACAGGTGATTTGTTTTGCATTCCATGACAGCAAGCTGCTGATGGAGACCTGCCAGGAGGCCAAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - -gctcctg
- - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - -gctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtat