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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttataggaaaattatgcctcattgttcattgttccgtaacaagctcgcaacattgtgtttatcaattctaccctgttcatgcatgtaaaaaag

Basic information

species Oryza sativa
transcript LOC_Os02g08544.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08544.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G433591_T02 (Zea mays), 5'ss of exon 6
GGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttataggaaaattatgcctcattgttcattgtt----ccgtaacaagctcgcaacattgtgtttatcaattctaccctgttcatgcatgtaaaaaag
|||| || || |||||||||||||| |||||||||||||||||||| || |||||||| ||||||||| ||||||| | |||||||||||||||||||||||| |  |  | ||| |  |      |||   |  |      ||   ||| ||| ||      |  |  | || || |    |  |  ||  |  || |   
GGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACCCAACATCCTCGGCTGAAAAGACCAAGAAGAAAAGgtatcacaatgaaaactgctttggtgttgcctaaggcgtaagcccagacaggcttgcc-tgcggcttgcaacattttttttttactactgttttcaacacg-

upper sequence: LOC_Os02g08544.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G433591_T01 (Zea mays), 5'ss of exon 6
GGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttataggaaaattatgcctcattgttcattgtt----ccgtaacaagctcgc-----------aacattgtgtttat-caattctaccctgttcatgcatgtaaaaaag------
|||| || || |||||||||||||| |||||||||||||||||||| || |||||||| ||||||||| ||||||| | |||||||||||||||||||||||| |  |  | ||| |  |      |||   |  |      ||   ||| ||| ||           |||||| | ||| | | | | |   |    | || |  |  |||        
GGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACCCAACATCCTCGGCTGAAAAGACCAAGAAGAAAAGgtatcacaatgaaaactgctttggtgttgcctaaggcgtaagcccagacaggcttgcctgcggcttgcaacattttttttttactactgttttcaacacgtggaattggaaacattgcag

upper sequence: LOC_Os02g08544.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G370332_T01 (Zea mays), 5'ss of exon 5
GGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttataggaaaattatgcctcattgttcattgttccgtaa-caagctcgcaacattgtgtttatcaattctacc----ctgttc-atgcatgtaaaaaag------------
| || || || ||||| || ||||| |||||||| |||||||||||||| |||||||| ||||||||| ||||||| ||||||||||| |||||||||||||| |  |  | ||  |  |      |||   |         |  || ||| |   | |    ||| |    | |||     |||||  |  |||||||||  |            
GATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACCCAACATCCTCGGGTGAAAAGACTAAGAAGAAAAGgtatcacaatgaaagctgctttgctgttgcctaaaccctgacaggcaggcttgtggcttgcccttttttttctgtacttgcactgttttaaacatgtaaaattggaaatgtcgcag

upper sequence: LOC_Os02g08544.3 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S154_83V6.1 (Physcomitrella patens), 5'ss of exon 9
GGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACCCAG------CATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttataggaaaattatgcctcattgttcattgttccgtaacaagctcgcaacattgtgtttatc---aattctac-cctgttcatgcatgtaaaaaag
      || |||||||| | || ||||||||||| ||||||||||| || |||||||| ||||| |||       |||| ||||     |||| |||   ||||| || | | | |    ||||     |  | ||| |   || |  || || |    |  |  ||||  | |   || || |    | ||| |  ||        |
------AATTGAAGCAAGTGAATAATTGGTTCATAAACCAACGCAAGCGGAACTGGCACAGCAATCCATTGTCATCATCTTCTGAGCTGAAGAGCAAACGGAAAAAgtgagt-acaccgtaattgcattttctggttgagcatttc-caagaaccgtctattaacgtgtcaacctcaaactccaggttttttcttttattcgttctcg

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|29640689|gb|CB645698.1|CB645698
EST:     AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAG                         AAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
genomic: AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttata ... tgtaaaaaagAAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
EST: gi|29640688|gb|CB645697.1|CB645697
EST:     AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAG                         AAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
genomic: AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttata ... tgtaaaaaagAAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
EST: gi|89185188|gb|CI050922.1|CI050922
EST:     AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCCAGAAGAAAAG                         AAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
genomic: AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttata ... tgtaaaaaagAAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
EST: gi|86488812|gb|CI131445.1|CI131445
EST:     AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACC---AAG--AAG                         -AA----A-AGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
genomic: AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttata ... tgtaaaaaagAAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
EST: gi|88408864|gb|CI554186.1|CI554186
EST:     AAAAGACCAAGAAGAAAAG                         AAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
genomic: AAAAGACCAAGAAGAAAAGgtaacttata ... tgtaaaaaagAAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
EST: gi|58691040|gb|CK079727.1|CK079727
EST:     AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAG                         AAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
genomic: AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttata ... tgtaaaaaagAAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
EST: gi|29663726|gb|CB660001.1|CB660001
EST:     AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAG                         AAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
genomic: AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttata ... tgtaaaaaagAAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
EST: gi|29661445|gb|CB657720.1|CB657720
EST:     AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAG                         AAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
genomic: AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttata ... tgtaaaaaagAAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
EST: gi|3760309|gb|C97565.1|C97565
EST:     AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAG                         AAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
genomic: AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttata ... tgtaaaaaagAAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
EST: gi|29670827|gb|CB667102.1|CB667102
EST:     AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAG                         AAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
genomic: AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttata ... tgtaaaaaagAAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
EST: gi|88225773|gb|CI225689.1|CI225689
EST:     AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAG                         AAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
genomic: AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttata ... tgtaaaaaagAAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
EST: gi|89195078|gb|CI051191.1|CI051191
EST:     AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAG                         AAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC
genomic: AACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttata ... tgtaaaaaagAAACGTTACAGGTGATGGTGGTGCTGAGCAATCGTGGTAGATTGGTTCAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACCCAGCATCCTCTGGTGAAAAGACCAAGAAGAAAAGgtaacttataggaaaattatgcctcattgttcattgttccgtaacaagctcgcaacattgtgtttatcaattctaccctgttcatgcatgtaaaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA