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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttagatgcaaatgctgaagatgcttttttgtcacaagagtttgtcaggcattcttatatcaaatgtatcattgcttctttttgtgtgttttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA

Basic information

species Oryza sativa
transcript LOC_Os04g55290.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55290.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G070451_T01 (Zea mays), 3'ss of exon 2
ttttagatgcaaatgctgaagatgcttttttgtcacaagagtttgtcaggcattcttatatcaaatgtatcattgcttctttttgtgtgt------tttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA
  | || | |   |   |   ||||   |         |  |  |  | || | ||||           | |||||||  |  |   | |      || |||||||| |  ||| ||||||||||||| || |||||||||||||| ||||| ||||||||||| || | ||||||||   ||||||||||||| || ||||    
--tcagtttcctctataggttatgcccctcaaatttgtgcctgggcaatgcctgcttaatctggcatcctgattgcttactgctacatctcccctcttgcagCCAGGTT-CGAGTGCCTTTGCTGTCTCCGGTGCATACAGACACGTGACCAAAACTTTGCAACGACCTATGTCTGCCACATCCCCAAGCATCTGAGGGAGGG---

upper sequence: LOC_Os04g55290.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G095670_T02 (Zea mays), 3'ss of exon 3
---ttttagatgcaaatgctgaagatgcttttttgtcacaagagtttgtcaggc-attcttatatcaaatgta-tcattgcttctttttgtgtgttttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA
   |||    |  |  |  ||  | | |   ||||| ||       || | |   |||||   |||     || | | |||| | ||| |     || |||||||| || ||||||||||| || || || |||||||| ||||| ||||||||||| ||||| ||||| |||||||| |||||||||||||| || ||||    
ctgtttcctctataggttatgctgct-caagtttgtgactgcgcaatgcctgcttattctagcatcctgattacttactgctacatttcgccctcttgcagCCAGGTTACGAGCGCCTTTGTTGCCTCCGGTGCATACAAACACGTGACCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG----

upper sequence: LOC_Os04g55290.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G020728_T01 (Zea mays), 3'ss of exon 3
-----ttttagatgcaa-atgctgaagatgcttttttgtcacaagagtttgtcaggcattcttatatca-aatgtatcattgcttctttttgtgtgttttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA
     |  |  || | | ||| |    | | ||     |    |  |  ||      | |||   |||   || | | | |||| | |||||     || |||||||| || |||||||||||||| || || |||||||||||||| || |||||||| ||||| ||||| |||||||| |||||||||||||| || ||||    
ttgtttcctgtatacgatatgttcctcaagtttgcgcctgggcaatgcctgct---taatctggcatcctgatttgttactgctacattttgccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTCCGGTGCATACAGACACGTGATCACAACTTCGCAACGACATGCGTCTGCCGCGTCCCCAAGCATCTGAGGGAGG----

upper sequence: LOC_Os04g55290.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G099007_T01 (Zea mays), 3'ss of exon 2
ttttagatgcaa-atgctgaagatgcttttttgtcacaagagtttgtcaggc--attcttatatcaa-atgtatcattgcttctttttgtgtgttttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA
 |||   | |   ||   |   ||| |  |         |  | ||    ||    |||   |||   || | | | |||| | ||||||    || |||||||| || |||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || ||||||||||| |||||||||||||| || ||||    
ctttgtttcctctatataggttatggtcctcaagtttgtggttgtgcagtgccagatctagcatcctcatttcttactgctacattttgtcctcttgcagCCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGAGTCCCCAAGCATCTGAGGGAGG----

upper sequence: LOC_Os04g55290.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 3
-------------ttttagatgcaaatgctgaagatgcttttttgtcacaagagtttgtcaggcattcttatatcaaatgtatcattgcttctttttgtgtgttttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA
             |||    |  |  |  ||||| |   |  ||||  |||       || ||||| || || ||       | | |||| | ||| |     || |||||||| || |||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || |||||||||||||||||||||||||| || ||||    
atgttttgctttgtttcctctataggttatgaagtt-tgtggttgt-gcaatgccagatctggcatcctcatttc-------ttactgctacatttggccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGGGTCCCCAAGCATCTGAGGGAGG----

upper sequence: LOC_Os04g55290.4 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3
ttttagatgcaaatgctga-agatgctt--ttttgtcacaagagtttgtcaggcatt--cttatatcaaatgtatcattgcttctttttgtgtgtttt-----cagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA
      |   | | ||||| |  |||||  |||    | ||||      ||   ||    ||| |||      ||| ||  ||  |  | ||  |||      |||||||| ||||| || || |||||  |  ||||||| ||  |||| || ||||||||||| || |||||||| ||||||||||||||||| || || ||||    
------aaaaacaggctgatatttgcttaatttctctaaaagataaaagcaaagatgaatttacatctccaaaatccttttttaatgatatgcttttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG----

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|88265420|gb|CI369194.1|CI369194
EST:     GCCTGGACCAGGGTTATGCAGACCGTAATCTGATTGCAAAGTGGAAAAAG                         GCTATGAGCGCCTTTGCTGTCTTCGATGCATACACACACGAGACCACAACT
genomic: GCCTGGACCAGGGTTATGCAGACCGTAATCTGATTGCAAAGTGGAAAAAGgttagtattt ... tttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACT
EST: gi|86505376|gb|CI148009.1|CI148009
EST:     GCCTGGACCAGGGTTATGCAGACCGTAATCTGATTGCAAAGTGGAAAAAG                         GCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACT
genomic: GCCTGGACCAGGGTTATGCAGACCGTAATCTGATTGCAAAGTGGAAAAAGgttagtattt ... tttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACT
EST: gi|88671806|gb|CI725341.1|CI725341
EST:     GCCTGGAACAGGGTTATGCACACCGTAATCTGATTGCCAAGTGGAAAAAGCCAG                      
genomic: GCCTGGACCAGGGTTATGCAGACCGTAATCTGATTGCAAAGTGG-AAAA---AGgttagtattt ... tttcagc
EST: gi|88228073|gb|CI227553.1|CI227553
EST:     GCTTGGACCAGGGTTATGCAGACCGTAATCTGATTGCAAAGTGGAAAAAGCCAG                      
genomic: GCCTGGACCAGGGTTATGCAGACCGTAATCTGATTGCAAAGTGG-AAAA---AGgttagtattt ... tttcagc
EST: gi|88532581|gb|CI462075.1|CI462075
EST:     AATCTGATTTGCAAAGTGGAAAAAGGCAG                      
genomic: AATCTGA-TTGCAAAGTGG-AAAA---AGgttagtattt ... tttcagc

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: 63 (upstream exon), 58 (downstream exon)
Score: 11

TGATCTTTATTACAGAAGGAAGGAGATATCAAAAGAGTTGTATGAGTTTTGCCTGGACCAGGGTTATGCAGACCGTAATCTGATTGCAAAGTGGAAAAAGgttagtattt ... tttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaggcattcttatatcaaatgtatcattgcttctttttgtgtgttttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA
                                          tgttttc  CT-rich tract
      attcttatatcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttagatgcaaatgctgaagatgcttttttgtcacaagagtttgtcaggcattcttatatcaaatgtatcattgcttctttttgtgtgttttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - -gatgcaa
- - - - - - -tgctgaa
- - - - - - - - - - gatgctt
- - - - - - - - - - - - - - - - -cacaaga
- - - - - - - - - - - - - - - - - - - - - - - - ggcattc