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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctggtattgattgaagtattaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT

Basic information

species Oryza sativa
transcript LOC_Os01g02090.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G051622_T02 (Zea mays), 3'ss of exon 5
ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctggtattgattg---aagtattaatacttttga-----gtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
  ||  || ||  ||   ||   |     ||||||||    ||| || |  || || | || | |    |||| | |    | || |     || | ||  |||||||||||| |||||||||||||  || ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| |||||||
--gagtat-ttgtataccttgggaa----atgatgct-tggattgaataatatttgttgttaaatagttaagtgtcagatttgttaatgtttgtatcttcctttgcagTTTTCACAGTCAGTAACAACATTCACTGAAGAATTTGATTTCACGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGAAAGAAAT

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G132796_T01 (Zea mays), 3'ss of exon 5
ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctggtattgattgaagtattaatacttttga-----gtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
  ||    || |  ||| |   |  |   ||||||||    ||| || |  || || ||   | | || | | |    | ||||     || | ||| |||||||||||| ||||| ||||||   || ||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||
--gagggagtatt-tgtataccttgggaaatgatgctagg-attgaataatat-tgttaaatagttaaatgtcagatttgttgatgtttgtatcttgctttgcagTTTTCACAGTCTGTAACAGCATTCACTGAAGAATTTGATTTCACGGCCATGAATGAGAAGTTTAACAAAGATGAAGTATGGGGCCATCTTGGTAAGAAAT

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
-ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctg--gtattga-ttgaagtattaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
   ||  ||  |  || |||| || |  || |  | ||  | || | |    |  ||   |||| | ||||  |  | | |  |||||   |  ||||| ||||  ||  |  ||||| ||||| || |||||||| ||||||||||  || |||||||||||||| || || |||||||| ||||||||||||||||| |   
ccagaaaattgtcaatattttgattttgttttctt-ctattgataagattataattgtaatattcagttgagttcatgaaaaatttga--ttaatgttt-gcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G11300.2 (Glycine max), 3'ss of exon 6
ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctg--gtattgattgaagtattaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
 |    ||||   || |  || |||| || |  | ||  | ||   |       ||    ||| | |  |||      |   || | |   |  ||||||||  || |||  |||| ||||| || ||||| || ||||||||||  || |||||||||||||| || || |||||||| ||||||||||||||||| |   
-tatatatgtaa-atatacttttatgtttttccttctattgatgggattatgattgtaacattcagttgagttcatgaaaaattcaattaatgcttttgcagGGTTTGCACCCAGTCACAAAATTCACTGAGGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G17050.1 (Glycine max), 3'ss of exon 6
ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctggta---ttgattgaagtattaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
|  |||       ||| |||||| |  |  |  | |   | ||   |       ||  |   |   ||||  |  | | |  ||  |   |  || |||||||  || ||   |||| ||||| || || || || |||||||| ||||| |||||||||||||| || || |||||||| ||||||||||||||||| |   
tatatctgtaaatatgcttttatttt-tcttccttccattgatgggattatgattgtaacattcagttgagttcatgaaaaattcaa--ttaatgctttgcagGGTTTGCGCCCAGTCACAAAATTCACAGAGGATTTTGATTTTATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G35640.1 (Glycine max), 3'ss of exon 6
ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctggtattgattgaagtat--taatacttttgagtctgttg--ttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
  | |   |||  || | | |||||   |||     |   |||  |     || |  |||  ||  || |||  || || |  || || |||||  ||||||||  | |  |  |||   || | |  ||||| || ||||||||   |||||||||||| ||||| || ||||||||||| ||||||  |||||| |||| | 
--ggtatagttatatatatatatatatatatatatatatatatatatatatattta-tatacatgtaaatatgatagtattggtgtgt-tgttgatttttgcagCCTCCATACACAGCTCCACAATACACTGAGGAGTTTGATTTTGAGGCCATGAATGAAAAGTTCAAAAAAGATGAAGTATGGGGTTCTCTTGGAAAGACAA

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G22680.3 (Glycine max), 3'ss of exon 4
ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctg--gtattgattgaagt--attaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
|  |||       ||| |||||| |  ||    | ||  | ||   |       ||    ||| | |  |||  || || | || |     |  || |||||||  ||  ||  |||| ||||| || ||||| || |||||||||||||| |||||||||||||| || || |||||||| ||||| ||||||||||| |   
tatatctgcaaatatgcttttatttttttccctt-ctattgatgggattatgattgtaacattcagttgagttcatgaaaaattcta---ttaatgctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------------ttgatcatgttt-catgtttttatatgattatgatgctgcttattaaagagcatctggtattgattgaagtattaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
                              |||     |||   ||||||||       |     || |   || || |  | ||  |     || |   ||  || ||  | | |||  |  || ||||   || ||   |||||  || || |||||||| ||||||||||  || ||||| || ||||| || || |||||||| |||||||||||||| ||||   
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctaccagtttaa-aatagctcatga-actttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv02s0087g00650.t01 (Vitis vinifera), 3'ss of exon 3
-ttgatcatgttt-catgtttttatatgattatgatgctgcttattaaagagcatctggtattgattgaagtattaatacttttgagtctgttg---ttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
   || ||  |   ||   ||| |  |   | || ||    ||  |||  |   | |     ||| |||||| | || | | |||  |||| ||   ||||||||| |  | |||| |      | || ||||||||||| ||||| || || |||||||| | |||||| || |||||||| |||||| ||||||| |||  | 
gaagaacacatccacagagtttcaggttgct-tggtgtgattt--taatcactgtataaatctgaatgaagtttcaa-attgttgc-tctggtgaatttttgcagTCTCAGAAGTCTGCTGTGCAGTTCACTGAAGAATTCGATTTTATAGCGATGAATGAAAGGTTTAAAAAGGATGAAGTTTGGGGTTATCTTGGAAAGGCAA

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
------ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctggtattgattgaagtattaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
      | | |    ||| |||     | ||  ||   |||  | || |  || |  |  ||| | |  |||| |   |   |  ||| |  |  |||  ||||||   || |   |||| ||||| || ||||| || |||||||||||||| ||||||||||| || || || |||||||| |||||||||||||||||     
ctattataggtttgattttatggggaga-atatttgcaatga-gtttctccaaaattaattggaaat--ttgacggcatggaatatttaa--catttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S35_195V6.1 (Physcomitrella patens), 3'ss of exon 7
--ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaag-agcatctggtattgattgaagtattaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
  ||| |   |||||   || |  ||  | | | | | | | || |   | ||||    | | || |  | | ||| ||    |||    |  || |  |||| |  || |  |   |    | || || ||||| ||||| ||||  ||||||||||||||||||||||| || ||||| |||||    |||||    ||  
tgttgtttg-gtttccgattatagtactactttcaagtttcatactttcgtagcaagacg-agtggtcaatg-attgatgtggttgtcaattgtgataagcagCTGGCGAATCCCACACAGCAATTCACAGAAGATTTTGACTTCACAGCCATGAATGAGAAGTTTAACAAGGACGAAGTTTGGGGAACCCTTGGGGGAAAGG

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|29668186|gb|CB664461.1|CB664461
EST:     CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCG                         TTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG
genomic: CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCGgtatgagtga ... tgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG
EST: gi|4879544|gb|AU063843.1|AU063843
EST:     CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCG                         TTTTCGCAGTCAGTANCAANTTTTACTGAAGANTTTGATTTCATGGCCATG
genomic: CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCGgtatgagtga ... tgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG
EST: gi|24208749|gb|AU225776.1|AU225776
EST:     CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCG                         TTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG
genomic: CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCGgtatgagtga ... tgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG
EST: gi|29670777|gb|CB667052.1|CB667052
EST:     CACACAGCAATCACCACTACAGGGGCCGTGGAAGAG-T------------                         TTT-CGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG
genomic: CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCGgtatgagtga ... tgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG
EST: gi|58660599|gb|CK049279.1|CK049279
EST:     CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCG                         TTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG
genomic: CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCGgtatgagtga ... tgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG
EST: gi|13896773|gb|AU183109.1|AU183109
EST:     CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCG                         TTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG
genomic: CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCGgtatgagtga ... tgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG
EST: gi|29668147|gb|CB664422.1|CB664422
EST:     CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCG                         TTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG
genomic: CACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCGgtatgagtga ... tgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATG

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: 66 (upstream exon), 75 (downstream exon)
Score: 31

TACAATGGAGCTGGTTCACACAGCAATCACCACTACAGGGGCCGTGGAAGAGGTAGAGGCAGCGCGgtatgagtga ... tgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagcatctggtattgattgaagtattaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
                        tattaat  putative branch site (score: 31)
                                            ttgtttt  putative PPT
                     aagtattaatactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctggtattgattgaagtattaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA