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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAATCCGTGCAACATCCTATTCTTCACATGAGATAGATGAGAATGAGAATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgctgcgttattattggacgtctgatttgccctaagttttgccagtaaacttgtgaagaattactgttttgattttttgacataatcactcgta...

Basic information

species Oryza sativa
transcript LOC_Os02g57510.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57510.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G101571_T02 (Zea mays), 5'ss of exon 3
CAGAATCCGTGCAACATCCTATTCTTCACATGAGATAGATGAGAATGAGAATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgctgcgttattattggacgtctgatttgccctaagttttgccagtaaacttgtgaagaattactgttttgattttttgacataatcactcgta---------
  ||||||| ||||||||||||||||| ||||||||||||||| | || ||||||  ||||||||||||| |||||||||| |||||||||||||||||||||   |||  | | |   |        | |      ||||  | ||    |    || || | ||  |||||   ||| || | | ||| | ||  |           
TGGAATCCGAGCAACATCCTATTCTTCTCATGAGATAGATGAGCAAGAAAATGATGGAGCTATTGATGGACTGCAGGATCGTGTCAGCATTCTCAAGCGGgtattgtgcaacttcaacttc------ttaaaacattctaa-ctctgttgattcttttatgtaaaacaactgt--agatattattatatacttaccagctcaagagatg
















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|88240546|gb|CI239708.1|CI239708
EST:     TCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: TCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
EST: gi|86259248|gb|CI010549.1|CI010549
EST:     ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
EST: gi|29677589|gb|CB673864.1|CB673864
EST:     ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
EST: gi|86594404|gb|CI251276.1|CI251276
EST:     ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
EST: gi|88206344|gb|CI206193.1|CI206193
EST:     ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
EST: gi|86501990|gb|CI144623.1|CI144623
EST:     ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
EST: gi|58690451|gb|CK079138.1|CK079138
EST:     ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
EST: gi|88966184|gb|CI013060.1|CI013060
EST:     ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
EST: gi|88202410|gb|CI201272.1|CI201272
EST:     ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
EST: gi|88832609|gb|CI008205.1|CI008205
EST:     ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
EST: gi|88902951|gb|CI088489.1|CI088489
EST:     ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
EST: gi|89197729|gb|CI013719.1|CI013719
EST:     ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
EST: gi|89180748|gb|CI009656.1|CI009656
EST:     ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGG                         TTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC
genomic: ATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgct ... gtacttgcagTTGTCTGGTGATATCCATGAAGAGGTGGAAACTCATAACCGTATGCTAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAATCCGTGCAACATCCTATTCTTCACATGAGATAGATGAGAATGAGAATGATCAAGCTATTGATGGATTGCAGGATCGAGTCAGCATTCTCAAGCGGgtaagttgctgcgttattattggacgtctgatttgccctaagttttgccagtaaacttgtgaagaattactgttttgattttttgacataatcactcgta

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA