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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaacctggaacctgttagctaatgatgtgattggcatgaattcccctgatttccaatgcttttactgaactgaacatcgttgaaattctggccttgtagAAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCAAAACTAGGCATAGGCAGGACCAAAGGCATTGCTGGAGGTGATGGTGACT

Basic information

species Oryza sativa
transcript LOC_Os02g52470.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G402242_T03 (Zea mays), 3'ss of exon 9
-----gaaacctggaacc-tgttagctaatgatgtgattggcatgaattcccctgatttccaatgcttttactgaactgaacatc-gttgaaattctggccttgtagAAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCAAAACTAGGCATAGGCAGGACCAAAGGCATTGCTGGAGGTGATGGTGACT
      | |  | ||||    |||  |     ||| |||    | |||||     |||| |  ||    |     ||||| |||  | ||||  ||||       ||||||||||||||||||| ||||||||||| ||||||||||||||||| || ||||||||||| || || |||||||    |||| ||| |||  ||||  
tactcaagatttcgaactgcattattttgctttgttattt---taaattcttaacattttctgtggaagt----tactgatcatttgatgaacctctgctgggacagAAATTATGCAAAGCATGCGTCTTGCTGGATGGATTGAATCGAGGCTTGCCGAAACTAGGCATTGGAAGTACCAAAGCAGGTGCTAGAGCTGACAGTGATG
















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|218487495|gb|FG946534.1|FG946534
EST:     GGATGCCAGAGCAAGGAACATGTGAACGTTGCGGCTACATTTCTAGTCAG                         AAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCA
genomic: GGATGCCAGAGCAAGGAACATGTGAACGTTGCGGCTACATTTCTAGTCAGgtatagtgat ... ggccttgtagAAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCA
EST: gi|29640585|gb|CB645594.1|CB645594
EST:     GGATGCCAGAGCAAGGAACATGTGAACGTTGCGGCTACATTTCTAGTCAG                         AAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCA
genomic: GGATGCCAGAGCAAGGAACATGTGAACGTTGCGGCTACATTTCTAGTCAGgtatagtgat ... ggccttgtagAAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCA
EST: gi|88466388|gb|CI529797.1|CI529797
EST:     CATTTCTAGTCAG                         AAGTTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCA
genomic: CATTTCTAGTCAGgtatagtgat ... ggccttgtagAAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCA
EST: gi|88903644|gb|CI089182.1|CI089182
EST:     GGATGCCAGAGCAAGGAACATGTGAACGTTGCGGCTACATTTCTAGTCAG                         AAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCA
genomic: GGATGCCAGAGCAAGGAACATGTGAACGTTGCGGCTACATTTCTAGTCAGgtatagtgat ... ggccttgtagAAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCA
EST: gi|218488923|gb|FG954497.1|FG954497
EST:     GGATGCCAGAGCAAGGAACATGTGAACGTTGTGGCTACATTTCTAGTCAG                         AAATTATGCAAAGCATGCGTCTTGCTGGACGGATTGAATCG
genomic: GGATGCCAGAGCAAGGAACATGTGAACGTTGCGGCTACATTTCTAGTCAGgtatagtgat ... ggccttgtagAAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgatttccaatgcttttactgaactgaacatcgttgaaattctggccttgtagAAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCAAAACTAGGCATAGGCAGGACCAAAGGCATTGCTGGAGGTGATGGTGACT
 ccctgat  putative branch site (score: 4)
                                   ttgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaacctggaacctgttagctaatgatgtgattggcatgaattcccctgatttccaatgcttttactgaactgaacatcgttgaaattctggccttgtagAAATTATGCAAAGCATGTGTCTTGCTGGACGGATTGAATCGAGGCTTACCAAAACTAGGCATAGGCAGGACCAAAGGCATTGCTGGAGGTGATGGTGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - gaacctg
- - - - - - - - - - - atgatgt
- - - - - - - - - - - - - - - - - gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaactg