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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATTGACAAGCTGATAGAAACTGGGGACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattcttttggcccctcttatgataattctaacatagaaagcttaatgccgaaaaaaaaaacatggtttaacctgaatttatggcttttgcag

Basic information

species Oryza sativa
transcript LOC_Os06g07200.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07200.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G021378_T01 (Zea mays), 5'ss of exon 10
ACAATTGACAAGCTGATAGAAACTGGGGACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattcttttggcccctcttatgataattctaacatagaaagcttaatgccgaaaaaaaaaacatggtttaacctgaatttatggcttttgcag
||||| ||||||||||||||||| || ||| | |||||||| ||||||||||| ||||| || ||||| || ||||||||||  || |||| ||||  |  |||   | | |    ||   |  ||  |||| || |||      |||||       |||||| | || ||  |||
ACAATCGACAAGCTGATAGAAACAGGCGACGGCGAGCAAATCTTTCAGAGAGCGATTCAAGAGCAAGGGCGAGGAAGGgtactaatcctttaggcc--ttctatacaactgcaggaatttcagcctggatgctgacaaagctgg-atggt-------gaatttcttgcattcacag

upper sequence: LOC_Os06g07200.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA16G27050.1 (Glycine max), 5'ss of exon 10
ACAATTGACAAGCTGATAGAAACTGGGGACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgatt---cttttggcccctcttatgataattcta-----acatagaaagctt------------aatgccgaaaaaaaaaacatggtttaacctgaatttatggcttttgcag---------------------------------------------
||||||||||   | || |||||||| || ||||| |||||||| ||||  ||||||||||||||||| || ||   ||| |  ||    || |||    ||| |   ||   ||        ||||   | |||            |||    | |  || | |||    | | || ||   |    |  | ||                                              
ACAATTGACAGATTAATTGAAACTGGAGATAGTGAACAAATTTTCCAGAAGGCTATTCAGGAACAAGGACGAGGCCAGgttcatatcttgctcttgctttctccttcaattcctcctcaaatgcatattcaactttttatattatccaatattaacatgaatatcattcactcatctaaacccaccattcatacaaacctaccttgccattgtacactcatagattgagttatctttgtag

upper sequence: LOC_Os06g07200.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv08s0032g00440.t01 (Vitis vinifera), 5'ss of exon 10
ACAATTGACAAGCTGATAGAAACTGGGGACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattcttttggcccctcttatgataattctaacatagaaagcttaa---tgccgaaaaaaaaaacatggtttaacctgaatttatggcttttgcag
||||||||||   | || || ||||| |||||||| |||||||| |||| ||| |||||||||||||| || ||   |||   |  ||||||      ||||     || ||     |       | ||     |    ||       | | |||||  | |  | |    |   | ||
ACAATTGACAGATTAATTGAGACTGGAGACAGTGAACAAATTTTCCAGAAAGCAATTCAGGAACAAGGACGAGGCCAGgt-ttgtctctttttctttttcttccctgaactcctttctcttttcttcaaattctcttggaatggtggaaagatttaatgttatataaaaaataaagaag

upper sequence: LOC_Os06g07200.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S496_4V6.1 (Physcomitrella patens), 5'ss of exon 9
ACAATTGACAAGCTGATAGAAACTGGGGACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattcttttggcccctcttatgataattctaacatagaaagcttaatgccgaaaaaaaaaacatggtttaacctgaattta-tggcttttgcag------------------------------------------------------------------------------
   |||||     |||| ||||| || |||||||||||||||||||| || ||||| ||||| || ||  | ||   ||||     |  |||||       |   |      |    |   |   | |    | |    | | |  || |||||  || |  || | ||||                                                                                    
GTCATTGAACGCTTGATTGAAACAGGAGACAGTGAGCAAATTTTTCAAAGGGCTATCCAGGAGCAGGGGAGAGGCCAGgtaaattatgctttggttaagaattgaactgccttggtttcttattttcataaaccactgcagacatttg-tttaatatgtaggtacttgcttaaatgtccaagacgaatgcagttgccgcttaaattttgtaactcccgttttgagccttcttcctattatgactgcgcggtgcag

upper sequence: LOC_Os06g07200.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ08209 (Selaginella moellendorffii), 5'ss of exon 7
ACAATTGACAAGCTGATAGAAACTGGGGACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattcttttggcccctcttatgataatt-ctaacatagaaagcttaatgccgaaaaaaaaaacatggtttaacctgaatttatggcttttgcag
||  |||||||| |||| |||||||| |||||||||  ||||||||| |  ||| |||||||||||||||| ||    |||   | |||||   ||    || |  |   | ||| |||    | | |    |                                            
ACTGTTGACAAGTTGATCGAAACTGGAGACAGTGAGACAATTTTTCAAAAGGCTGTTCAGGAACAAGGCCGAGGCCAAgtaagcactctttgatcctgcattttctttgctgctagcatcactatcctcgctctag-----------------------------------------

upper sequence: LOC_Os06g07200.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ12216 (Selaginella moellendorffii), 5'ss of exon 7
ACAATTGACAAGCTGATAGAAACTGGGGACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattcttttggcccctcttatgataatt-ctaacatagaaagcttaatgccgaaaaaaaaaacatggtttaacctgaatttatggcttttgcag
||  |||||||| |||| |||||||| |||||||||  ||||||||| |  ||| |||||||||||||||| ||    |||   | |||||   ||    || |  |   |  || |||    | | |    |                                            
ACTGTTGACAAGTTGATCGAAACTGGAGACAGTGAGACAATTTTTCAAAAGGCTGTTCAGGAACAAGGCCGAGGCCAAgtaagcactctttgatcctgcgttttcttttctgttagcatcactatcctcgctctag-----------------------------------------

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|117224830|gb|CT845929.1|CT845929
EST:     ACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGG                         GTGCTTGACACTCTCCAAGAAATTCAGGAACGGCATGATGCAGTGAAAG
genomic: ACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattc ... gcttttgcagGTGCTTGACACTCTCCAAGAAATTCAGGAACGGCATGATGCAGTGAAAG
EST: gi|86878358|gb|CI319605.1|CI319605
EST:     ACAAGCCCGT-GAAGG                         GTGC-TGACACTCTCCAAGAAATTCAGGAACGGCATGATGCAGTGAAAGAG
genomic: ACAAGGCCGTGGAAGGgtaccgattc ... gcttttgcagGTGCTTGACACTCTCCAAGAAATTCAGGAACGGCATGATGCAGTGAAAGAG
EST: gi|27548906|gb|CA767571.2|CA767571
EST:     ACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGG                         GTGCTTGACACTCTCCAAGACATTCAGGAACGGCATGATGCAGTGAAAGAG
genomic: ACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattc ... gcttttgcagGTGCTTGACACTCTCCAAGAAATTCAGGAACGGCATGATGCAGTGAAAGAG
EST: gi|319908621|gb|HS977749.1|HS977749
EST:     ACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGG                         GTGCTTGACACTCTCCAAGAAATTCAGGAACGGCATGATGCAGTGAAAGAG
genomic: ACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattc ... gcttttgcagGTGCTTGACACTCTCCAAGAAATTCAGGAACGGCATGATGCAGTGAAAGAG
EST: gi|18385545|gb|BM418744.1|BM418744
EST:     ACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAA-GCCGTGGAAGG                         GTGCTTGACACTCTCCAAGAAATTCAGGAACGGCATGATGCAGTGAAAGAG
genomic: ACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattc ... gcttttgcagGTGCTTGACACTCTCCAAGAAATTCAGGAACGGCATGATGCAGTGAAAGAG
EST: gi|18386037|gb|BM419236.1|BM419236
EST:     TGAGCNAATTTTTCAGAGAGCTATTCAGGAACAA-GCCGTGGAAGG                         GTGCTTGACACTCTCCAAGAAATTCAGGAACGGCATGATGCAGTGAAAGAG
genomic: TGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattc ... gcttttgcagGTGCTTGACACTCTCCAAGAAATTCAGGAACGGCATGATGCAGTGAAAGAG

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), 57 (downstream exon)
Score: 9

ACAATTGACAAGCTGATAGAAACTGGGGACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattc ... gcttttgcagGTGCTTGACACTCTCCAAGAAATTCAGGAACGGCATGATGCAGTGAAAGAGATAGAGCAGAAGCTTCTTGAGCTGCAACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATTGACAAGCTGATAGAAACTGGGGACAGTGAGCAAATTTTTCAGAGAGCTATTCAGGAACAAGGCCGTGGAAGGgtaccgattcttttggcccctcttatgataattctaacatagaaagcttaatgccgaaaaaaaaaacatggtttaacctgaatttatggcttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG