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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctctgctctgcttgtgttgtttttcttttctgagaacagccatatgagatggatttaaaaatcatgtgattgatgaatgatctgaaatttcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCTAGGATTATAAGTGTTACCAGTGAGGAATCAGAGTAACGAAGAGATCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g07960.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07960.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G124270_T01 (Zea mays), 3'ss of exon 2
----------gctctgctctgcttgtgttgtttttcttttctgagaacagccatatgagatggatttaaaaatcatgtgattgatgaatgatctgaaatttcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCTAGGATTATAAGTGTTACCAGTGAGGAATCAGAGTAACGAAGAGATCAAG
           | ||  |    |    |||    ||||||||   || | ||||    |||| ||| ||   |||    | ||||      ||| |||| | || ||||||||| |||||||||||| ||| |||||||  | || ||||||||||||||||||||| || ||| ||  ||||||| |||||||| || || | |  | |
gtttttctattcactattgcattctgtttggcaatcttttctagaaata-ccat----gatgcattcaaggttcactctactgatc-----tctcaaatctattgtgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCTAGGATTGTAGGTGCTAGTAGTGAGGTATCAGAGTGACAAATAAAGGAGG

upper sequence: LOC_Os02g07960.2 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G335638_T01 (Zea mays), 3'ss of exon 16
gctctgctctgcttgtgttgtttttcttttctgaga--acagccatatgagatggattt---aaaaatcatgtgattgatgaatgatctgaaatttc-ttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCTAGGATTATAAGTGTTACCAGTGAGGAATCAGAGTAACGAAGAGATCAAG
       | |  |||| ||  ||||  | |   | |   ||  |   | ||     |||   ||||||     |||  ||  | | |    | |||  |||||||||||| |||||||||||| ||| |||||||  | || ||||||||||||||||||||| || ||| ||   ||| || |||||||| ||  | | |    |
------ttgtatttgtttttatttttctattcaatattgcattctggttagcgctcttttctaaaaataccaagatgcattcaaggttcacacttttattatgcagCCGGGACCAGAATTCAGGCCAGCAATGTCTCAAATCGTCCAAGACCTAGCTAGGATTGTAGGTGCTAGTGGTGCGGTATCAGAGTGACAGATAAAGGGGG
















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|29621906|gb|CB626917.1|CB626917
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|88964295|gb|CI045488.1|CI045488
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|88990504|gb|CI107891.1|CI107891
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|58687945|gb|CK076632.1|CK076632
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|29656568|gb|CB652843.1|CB652843
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|86603302|gb|CI112062.1|CI112062
EST:     ATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: ATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|29626065|gb|CB631076.1|CB631076
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|29626028|gb|CB631039.1|CB631039
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGC                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|3769154|gb|AU033181.1|AU033181
EST:     CAGACATCCATCAGCCNTTGTATCCGG                         CCGGAACCCAGAATTCAGACCATCAATGTCAGAGATTGNCCAAGACCTAGC
genomic: CAGACAT-CATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAA-CCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGC
EST: gi|29640907|gb|CB645914.1|CB645914
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|66927345|gb|CX114193.1|CX114193
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|29674397|gb|CB670672.1|CB670672
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|29671438|gb|CB667713.1|CB667713
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|29638004|gb|CB643013.1|CB643013
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|29631499|gb|CB636508.1|CB636508
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
EST: gi|58690978|gb|CK079665.1|CK079665
EST:     CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGG                         CCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT
genomic: CTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCT

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: 75 (upstream exon), 21 (downstream exon)
Score: 3

CATTGAGTCCATATCAAAGATGGTTGATCCTTCTATTCAAGGAGAGTGTTCTGAGAAAGTACTGTCACGTTTTGCAGACATCATCAGCCGTTGTATTCGGgtaatcaaat ... tcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCTAGGATTATAAGTGTTACCAGTGAGGAATCAGAGTAACGAAGAGATCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagatggatttaaaaatcatgtgattgatgaatgatctgaaatttcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCTAGGATTATAAGTGTTACCAGTGAGGAATCAGAGTAACGAAGAGATCAAG
                       gattgat  putative branch site (score: 3)
                                           tttcttat  putative PPT
        atttaaaaatcatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctctgctctgcttgtgttgtttttcttttctgagaacagccatatgagatggatttaaaaatcatgtgattgatgaatgatctgaaatttcttatgcagCCGGAACCAGAATTCAGACCATCAATGTCAGAGATTGTCCAAGACCTAGCTAGGATTATAAGTGTTACCAGTGAGGAATCAGAGTAACGAAGAGATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA