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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCAGGCTCCAGAGGGTAACCATAAACTGACAAAGGCAGAGGCAATGAATCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttgttttaaacaaactatgggggtgtttagatctaggggtgtaaaattttggtgtgtcacatcaagtattatatagggtgtcgcatggggtgt...

Basic information

species Oryza sativa
transcript LOC_Os06g02550.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02550.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM5G864414_T02 (Zea mays), 5'ss of exon 18
-TGTCAGGCTCCAGAGGGTAACCATAAACTGACAAAGGCAGAGGCAATGAATCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttgttttaaacaaactatgggggtgtttagatctaggggtgtaaaattttggtgt-gtcacatcaagtattatatagggtgtcgcatggggtgt
 |  |||   | | |     |  ||||  ||||||||||||| || ||||| ||| ||||||||||||||            ||||||||||||||||||||| ||| ||| |  |   | | | || || | | || | |   |     | ||| ||| | | || ||||   | | | |    ||| ||  |   |    
CTCCCAGAGACTA-ATAACCATAATAAGGTGACAAAGGCAGAAGCGATGAACCAGTCTTGGTCCAGACCA------------GCAGCAGTAAGGAGCAATGgtaagtattggtc-atgaacattgtgtggctctatataccctaga----acaatcttgttttagtaacattgcgaacttt----ggtatctgagcag----
















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|86827901|gb|CI274841.1|CI274841
EST:     TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|29638209|gb|CB643218.1|CB643218
EST:     TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|58685705|gb|CK074392.1|CK074392
EST:     TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|88908091|gb|CI090687.1|CI090687
EST:     GGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: GGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|88226381|gb|CI226297.1|CI226297
EST:     ACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: ACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|88833179|gb|CI076662.1|CI076662
EST:     TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCAGTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|66916087|gb|CX102935.1|CX102935
EST:     TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|218489541|gb|FG952487.1|FG952487
EST:     AGCCTTGGTCCAGACCGA-CACCAGCAGCTAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCAGTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: AGCCTTGGTCCAGACC-ACCACCAGCAGC-AGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|86479184|gb|CI121817.1|CI121817
EST:     CAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: CAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|29641487|gb|CB646494.1|CB646494
EST:     TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|218496116|gb|FG953480.1|FG953480
EST:     CCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: CCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|58593890|gb|CF992198.1|CF992198
EST:     TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGTGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|29666198|gb|CB662473.1|CB662473
EST:     TCAGCCTTGGTCCAGACCACCTCCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|29626826|gb|CB631837.1|CB631837
EST:     TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|58684250|gb|CK072937.1|CK072937
EST:     TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGTGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|29626870|gb|CB631881.1|CB631881
EST:     TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
EST: gi|58688578|gb|CK077265.1|CK077265
EST:     TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATG                         GAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA
genomic: TCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttg ... ccttatgtagGAAATTACTTCACTAAAGACCAGGGCCCTCGTGCGCCTGACATTGCGGAGA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCAGGCTCCAGAGGGTAACCATAAACTGACAAAGGCAGAGGCAATGAATCAGCCTTGGTCCAGACCACCACCAGCAGCAGCAGCAGTAAGGAGCAATGgtgagtgttgttttaaacaaactatgggggtgtttagatctaggggtgtaaaattttggtgtgtcacatcaagtattatatagggtgtcgcatggggtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggggtg