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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaatatagtccaaggttgtattttgattatgttcatgttcaacctccaagactgttggtagcatcggtttataagcgtcaacaattgtgttcc...

Basic information

species Oryza sativa
transcript LOC_Os03g01150.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01150.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G374779_T04 (Zea mays), 5'ss of exon 6
TTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaatatagtccaaggttgtattttgattatgttcatgttcaacctccaagactgttggtagcatcggtttataagcgtcaacaattgtgttcc
|||||| ||||||||||| |||||||||||  | |||| | ||||||||||||||||||||||||| || || |||||||||||||||||  | || |||||||| || | || |||  |      | |  ||||   ||| |  |  ||||   |   |  |    | ||   | |||    || |      |      
TTGTAGGTTTCTTCCAAAACTTAACAATGAAATTCCAGATAAAAGAAATGCCACCTACAAGGAAAGATTCAGTAGCTTAGAGAATTTGGTTCTGATTATGgtaagcttgacatggtctgaatccaaaatc-gattgaattctt--ttgacct---atcttaatatatgtatgtatgtatgtatgttatttgcag------

upper sequence: LOC_Os03g01150.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA01G41570.1 (Glycine max), 5'ss of exon 10
TTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagt--ttaatatagtccaaggttgtattttgatta---tgttcatgttcaacctcc--aagactgttggtagcatcggtttataagcgtcaacaattgtgttcc
 |||||||||||||||  ||||||||||||  |||||| | | |||||| | || ||||||||||| ||||| |||||  ||||||||||| | ||||||||||||  |  | ||        ||  |||| ||| ||   | ||  |  |  |  ||   | ||  | |  ||   | |   | | |   |  ||| |        
CTGTAGATTTCTTCCAGTGCTTAACAATGAAATACCAGATAAGAGAAATTCTACTTACAAGGAAAGATTTAGTAGCTTGCAGAATTTGGTACTTATCATGgtaagtcctctaaatgtatttttgtgatattatgaatagaatattgctaattgatttcatgaggaaagcttatatatttgtaatcttattttatacattaacag---

upper sequence: LOC_Os03g01150.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv02s0488g00020.t01 (Vitis vinifera), 5'ss of exon 9
TTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaa------tatagtccaaggttgtattttgatta-tgttca------tgttcaacctccaagactgttggtagcatcg--gtttataagcgtcaacaattgtgttcc----------------------
 ||||||||||| ||||||||||| |||||  | || | ||| || ||| | || ||||||||| | || || |||||||||||||||||  | |||||||| |||| ||      | |  |||   | | ||  |   ||| |  |||      |||||    | |   | |  ||   |  | |  ||| |  |   |  | | |||    |                       
ATGTAGATTTCTACCAAAGCTTAATAATGAACTCCCTGATGAGAGGAATTCAACTTACAAGGAACGTTTCAGTAGCTTAGAGAATTTGGTTCTTATCATGgtgagttgaaagagctttttctcccttgctataactctcttagtcctcagattattgttctctttactcaatttatgcaggtttagctgttcaagaatatttatatttgccaccttatcatattggtttctcaacag

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|29619262|gb|CB624274.1|CB624274
EST:     CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATG                         TTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC
genomic: CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaa ... taatgtttagTTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC
EST: gi|44667871|gb|CR281305.1|CR281305
EST:     CCACCTACAAGGAAAGGTTTACCAGCTTAGAGAATTTGGTATTAATCATG                         TTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC
genomic: CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaa ... taatgtttagTTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC
EST: gi|66916126|gb|CX102974.1|CX102974
EST:     CCACCTACAAGGAAAGGTTTAGCAGCTTAAAGAATTTGGTATTAATCATG                         TTTCAAGATGACGCTGTCTTGATACCTCGGGAAACAACATGGTTTGGTTAC
genomic: CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaa ... taatgtttagTTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC
EST: gi|29661631|gb|CB657906.1|CB657906
EST:     CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATG                         TTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC
genomic: CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaa ... taatgtttagTTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC
EST: gi|29619263|gb|CB624275.1|CB624275
EST:     CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATG                         TTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC
genomic: CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaa ... taatgtttagTTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC
EST: gi|29661632|gb|CB657907.1|CB657907
EST:     CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATG                         TTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC
genomic: CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaa ... taatgtttagTTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC
EST: gi|25797306|gb|CA753267.1|CA753267
EST:     CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTAT-AATCATG                         TTTCAGGATGACGCTG
genomic: CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaa ... taatgtttagTTTCAGGATGACGCTG
EST: gi|3766554|gb|AU030664.1|AU030664
EST:     CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATG                         TTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC
genomic: CCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaa ... taatgtttagTTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTAC

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: 64 (upstream exon), 70 (downstream exon)
Score: 29

TTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaa ... taatgtttagTTTCAGGATGACGCTGTCTTGATACCTCGGGAAACAGCATGGTTTGGTTACTATCCAGATGGAGGTTTCGATCCTGTCCTGCCCCCTCAGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCTTAGAGAATTTGGTATTAATCATGgtaagtttaatatagtccaaggttgtattttgattatgttcatgttcaacctccaagactgttggtagcatcggtttataagcgtcaacaattgtgttcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT