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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacatgcatttatgtgatattaactttcgttgacccaacctattccttcccttgttttattcaaattacaactaattcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA

Basic information

species Oryza sativa
transcript LOC_Os01g71280.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 2
gacatgcatttatgtgatattaactttcgttgacccaacctattccttcccttgttttattcaaattacaacta-attcagcattttaa--aataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
  |||    ||      ||| |||  |  ||    |  | || | |||  | || ||  || | || |  | || |  | |  ||||||  |||  ||||||||||||||||||||||| |||||||| ||||||||||| |||||||| ||||| || ||||||||||||||||||||||| |||||||||||||| |||||
-gcatctggttgaaacgtataaacagttttt--ttctgcttaatgcttggcctgcttatttgagatcagcagtacagactgatttttaaggaatgcattgcagCTGGAGTTCCAACTGAAAATATACTCTATCTTGGAGGACCAAACATCGCCTCGGAAATTTATAACAAAGAATATGCAAACGCTCGAATCTGTGGATCCAA

upper sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 1
gacatgcatttatgtgatattaactttcgttgacccaacc-tattccttccc--ttgttttattcaaattacaactaattcagcattt-taaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
        ||||  | |  |||| ||| |||| |       || |   | |    |   | |||    || || |   ||||   | | ||  ||   ||| ||||||||| || | |||||| || || || |||||||| || |||||||||||||| ||||| ||||| ||||||||||| ||| | || |||||| |  |
---gaatttttaattcagtttaa-ttttgttggcatgtttatagtttatactaactaaatgattttttttccatccccttcactgtctctatcatgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAACGCTAGGATATGTGGGGCAGA

upper sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 1
-gacatgcatttatgtgatattaactttcgttgacccaacctattccttcccttgttttattcaaattacaactaattc--agcatt-ttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
  | |   || |   |||||||   ||  |  |  |  |  | |    |      |   || ||  ||  |   || ||  | | ||     | |   |||||||||| |||||    || |  || || ||||||||||| || |||||||||||||| ||||| ||||| ||||||||||||||||| || |||||| |  |
gaaaaaaaatct---tgatattc-tttctggagttcttatttttgtaatggtacatgacatccatgtttaattaaactcccatcgttgcctgatttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA

upper sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G15900.1 (Glycine max), 3'ss of exon 1
gacatgcatttatgtgatattaactt-------tcgttgacccaacc-tattccttcccttgttttattcaaattacaactaattcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
     | |||||| |||||  |||           | | |   |    |||  ||     | | || |   | |  |||||   |   || || | | |   |  |||||||||| || |  ||||| ||||| |||||||| || ||||| ||||||||||| || || ||||| || ||||| ||||||||||| || ||  |  |
----agaatttatttgataccaaccaatagaagctgataatttagtagtatatctatttctatattttctcattctcaact--ctttacaattcatact--ttgacagCTGGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCTCGAATATGCGGAGCAGA

upper sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G33340.1 (Glycine max), 3'ss of exon 1
gacatgcatttatgtgatattaactttcgttgacc--caacctattccttcccttgttttattcaaattacaactaattcagcattttaaaataaatt-----gcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
     | |||| | |||||   ||    |    |    ||  |  |  |     | ||||  ||   || |  |    ||| |  |||| |||  ||       |||||||||| || |  ||||| ||||| |||||||| || ||||| ||||||||||| || || ||||| || ||||| ||||| ||||| || ||     |
----agaatttgtttgataacgaccaatggaagctggtaatttggtagtatatctatttttatc---tttcctcattctcaactctttacaatgcatactttgacagCTGGAGTGCCTATGGAGAACATACTGTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCCCGAATTTGCGGAGATGA

upper sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G28970.1 (Glycine max), 3'ss of exon 1
gacatgcatttatgtg-atattaactttcgttgacccaacctat-tccttcccttgttttattcaaattacaactaat-tcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
 | |  | ||| | |  || | | ||    |||    | | ||  || |  |||| ||    |  ||| | | ||| | |  |||||  ||| |  ||   |||| |||| || |  ||||| ||||| |||||||| || ||||| ||||||||||| || || ||||| || ||||| |||||  ||||||||||  |  |
aatactcttttttatttatttcatctgattttgtattatcataggtcatagccttcttaccatgcaataatatctattctttgcattgcaaacttgat---agCTAGAGTGCCTATGGAGAACATACTCTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATCTGTGGAGCTGA

upper sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
--gacatgcatttatgtgatattaactttcgttgacccaacctattccttc--ccttgttttattcaaattacaactaattcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
   |  |   | |   |  | ||     |  |  |   |  |||||    |   |||| ||  ||     |  || |  |||   | |||    |   | | |||||| || || | ||| ||| | || |||||||| || |||||||||||  | || ||||| ||||| |||||||| |||||| ||||||||||  |   
gtaagctttttcttcttccttttgctccttttatattgagtctattgacacaatcttgcttagtttt--cttgaattggttct-tactttggtgtttgtggtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGC

upper sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 1
--gacatgcatttatgtgatattaactttcgttgacccaacctattccttcccttgttttattcaaattacaactaattcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
    ||    | | |||  | || | ||    | |   |  | |    ||   || |  | |    | | |   |   |||  ||| ||   |   |||||||||||||||| |  |||||||| || |||||||| || || || ||||||||||| ||||| ||||| ||||| || |||||||| || |||||  |  |
tcaccacat-tctctgtagtttttatttgtcctaattgatgccaccttttttattttactttctccacttct-ttgcctcattattatattgtgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA

upper sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------gacatgcatttatgtgatattaactttcgtt---gacccaacctattcctt----cccttgttttattcaaa----ttacaacta--attcagcattttaaaataaatt--------gcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
                                       | ||  | |||||  | ||   | |   |    |  | |  |||| |||    |  |||  |||   | |    |||   |||  ||  |    |||   ||| ||         |||||||| ||  | |  || || || || || |||||||| ||||||||||||||||||||||| ||||| || ||||| ||||||||||| |||||  |  |
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA

upper sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S323_18V6.2 (Physcomitrella patens), 3'ss of exon 3
-gacatgcatttatgtgatattaact--ttcgttgacccaacctattccttcccttgttttattcaa--attacaactaattcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
  || ||  | | | || ||| | ||  || |||     ||    |    |    ||  ||  |  |  ||| ||||| | |      |     ||    | |||| ||||| ||  |||||||| | |||||||||||||| ||||| ||||| || ||  |||||||||| || || || ||||| || |||||||||||  |
tcacttgtgtgtgtatg-tatcatctaattggtttttttaaaaagtgtaataagatgagttgcttgagaattgcaactgact----ggtgggggatgtgattcagCCGGAGTGCCTTCTGAGAATGTCCTATATCTTGGAGGTCCAAATATTGCTTCTGAAGTTTATAACAAGGAGTACGCCAATGCACGGATCTGTGGGTCAGA

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|300215932|gb|HO088558.1|HO088558
EST:     GGACCCAATTCCTCGTATCATTACGCCCACGCAGATGATTAGTTCTGCAA                         CTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCT
genomic: GGACCCAATTCCTCGTATCATTACGCCCACGCAGATGATTAGTTCTGCAAgtaagcagct ... taaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCT




















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: 48 (upstream exon), 70 (downstream exon)
Score: 6

ATCAGCGTTCCGGTGATAATCTCGCTCGCAAAGGGGATAGAAGCATCCTTGGACCCAATTCCTCGTATCATTACGCCCACGCAGATGATTAGTTCTGCAAgtaagcagct ... taaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcccttgttttattcaaattacaactaattcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
                        aactaat  putative branch site (score: 6)
                 aaattacaactaattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacatgcatttatgtgatattaactttcgttgacccaacctattccttcccttgttttattcaaattacaactaattcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
-acatgca
- - - - - - tgtgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcagca