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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGGATGAAATTAACAGGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtcttattcatggacataagttcatatatgatttttccctctatgcaatggtgaatctttgttaggaacaatgaaacctgccttttcaagaaaa...

Basic information

species Oryza sativa
transcript LOC_Os03g24460.3
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24460.3 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G108416_T01 (Zea mays), 5'ss of exon 17
TGTTGGATGAAATTAACAGGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtcttattcatggacataagttcatatatgatttttccctctatgcaatggtgaatctttgttaggaacaatgaaacctgccttttcaagaaaa
                   ||||||||||||||||| ||||| | | | |||||||||||||| ||||||||| | |||||||| ||||||||||| |||||      |||       | |||   |  ||  |  |    |     |  ||    |             | |      |    ||  ||          
-------------------GTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtactttacttaagccatgtttgaatgcactagagctaatagttagccgctgcaggcgcggacgcgcatggccaaggtgtgtgttgctgctgccg

upper sequence: LOC_Os03g24460.3 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G108416_T02 (Zea mays), 5'ss of exon 1
TGTTGGATGAAAT-TAACAGGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtcttattcatggacataagttcatatatgatttttccctctatgcaatggtgaatctttgttaggaacaatgaaacctgccttttcaagaaaa
  |   ||||||  ||||||||||||||||||||||| ||||| | | | |||||||||||||| ||||||||| | |||||||| ||||||||||| |||||      |||       | |||   |  ||  |  |    |     |  ||    |             | |      |    ||  ||          
-CTCAAATGAAAAATAACAGGTCATGGATCTTGTGGTGAAAGAAAACTTTGTGTTACATGAACGACGCATTAGTCTGTCAGAATTCCATGCTGCAGATGAGgtatggtactttacttaagccatgtttgaatgcactagagctaatagttagccgctgcaggcgcggacgcgcatggccaaggtgtgtgttgctgctgccg
















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|89187323|gb|CI047390.1|CI047390
EST:     TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88278817|gb|CI397621.1|CI397621
EST:     CGCATTAGTTAATCAGAATTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: CGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88542896|gb|CI472254.1|CI472254
EST:     CTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: CTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|86869013|gb|CI335580.1|CI335580
EST:     TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88828489|gb|CI073359.1|CI073359
EST:     TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGGAATCACACCG
genomic: TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88957211|gb|CI095197.1|CI095197
EST:     TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88263285|gb|CI367059.1|CI367059
EST:     TGTTACAT-AACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88437450|gb|CI528809.1|CI528809
EST:     TTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: TTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88958377|gb|CI095895.1|CI095895
EST:     TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88525458|gb|CI453913.1|CI453913
EST:     ATTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: ATTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88531544|gb|CI460026.1|CI460026
EST:     CATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: CATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|86433061|gb|CI093404.1|CI093404
EST:     TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|86426440|gb|CI071537.1|CI071537
EST:     TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88541495|gb|CI470767.1|CI470767
EST:     TGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: TGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88278792|gb|CI397596.1|CI397596
EST:     CGCATTAGTTTATCAGAATTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: CGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88548475|gb|CI476851.1|CI476851
EST:     TTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: TTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG
EST: gi|88964563|gb|CI069911.1|CI069911
EST:     TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAG                         GTATGGACTACTGGAACGATGGGTGAAATCACACCG
genomic: TGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtct ... tcacctgcagGTATGGACTACTGGAACGATGGGTGAAATCACACCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGGATGAAATTAACAGGTCATGGATCTTGTGGTAAAAGAGAGCCTGGTGTTACATGAACGTCGCATTAGTTTATCAGAATTTCATGCTGCAGACGAGgttccagtcttattcatggacataagttcatatatgatttttccctctatgcaatggtgaatctttgttaggaacaatgaaacctgccttttcaagaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG