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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgttttcctgttctctcttaggcttgtcatgtataaaagaaaatgagaataataaaacagtttggtcttaggtatgcagcgagcgatgactaaaaa...

Basic information

species Oryza sativa
transcript LOC_Os01g56630.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G078576_T04 (Zea mays), 5'ss of exon 16
ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgttttcctgttctctct-taggcttgtcatgtataaaagaaaatgagaataataaaacagtttggtcttaggt--atgcagcgagcgatgactaaaaa
|||||||| ||||| ||||||||||||||||||||||| || |||||||| || ||||||||||||||||||||| ||||||| ||||| |||||||  |||  |||||| | | |  || | |  ||| |     | |||| |  |      |    |||    || ||  ||  |      ||  | ||    
ATGTTTACTCAGTTGCGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAATTCTTTATCCCATATGCATGGCGCCTTGTCCTGTCACGGGGgtaatcattttttgttctatatgttagcatattgtgtttgtgt-ataatgggccttggcccatgtcttgactatatgttaatatattccctgaccattagg--

upper sequence: LOC_Os01g56630.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G079389_T01 (Zea mays), 5'ss of exon 16
ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgttttcctgttctctcttaggctt---gtcatgtataaaagaaaatgagaataataaaacagtttggtcttaggtatgcagcgagcgatgactaaaaa
|||||||||||||||||||||||||||||||||||||| || ||||||||||| || |||||||||||||||||| ||||||||||||| |||||||  ||| ||||| | |    |  |    ||  | ||          | | ||  || | || |||   | ||    |  |   || |  |         
ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGCCACCCTGAGGAGTTCTTCATCCCATATGCATGGCGCCTTGTCCTATCACGGGGgtaatcatttgctgttatatagatgattcacagttttttactccctccgtttataaatatgacactgttgacttttttaaaaactttgatcattcgtctt---

upper sequence: LOC_Os01g56630.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA10G00550.1 (Glycine max), 5'ss of exon 16
ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgttttcctgttctctcttaggcttgtcatgtataaaagaaaatgagaataataaaacagtt-tggtcttaggtatgcagcgagcgatgactaaaaa-
|||||||| ||  | |  || |||||||| ||||| ||||| || ||||||||||||||||||||||  ||||   | || |||||  || ||||  ||| |   | |   | ||    ||  | |   |    |  | |   ||   |    || || | || | |  | ||  |      |||  |      
ATGTTTACTCAACTTCATTTCACATATGAACAAGAGAGTCACCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTACTATCCAGATGgtatggttctagagattcttattta--ttcacttacttcgtggctatttgtaactgtttttcacttgtagtatgaactttgttgttcttaatgcatgtggtt

upper sequence: LOC_Os01g56630.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA10G38920.2 (Glycine max), 5'ss of exon 16
ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgttttcctgttctctcttaggcttgtcatgtataaaagaaaatgagaataataaaacagtttggtcttaggtatgcag--cgagcgatgactaaaaa
|||||||| ||  | || || |||||||| ||||| |||||||| ||||||||||||||||||||||  ||||   | || ||||| ||  |||| || || |  |  || |  ||  |   |  | | |||    | ||   | || |  |    |    | | |  | ||  |  |          | |  |
ATGTTTACTCAACTGCGCTTCACATATGAACAAGAGAGTCATCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTGCTATCCCGTTGgta-tgattcctggagcttttctattcacattgtct-taaggctacatataattattttactcttacattttgaattgtgttggccttatttcatttcatta

upper sequence: LOC_Os01g56630.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA20G28880.1 (Glycine max), 5'ss of exon 15
ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgttttcctgttctctcttaggcttgtcatgtataaaagaaaatgagaataataaaacagtttggtcttaggtatgcagcgagcgatgactaaaaa--
|||||||| ||  | || || |||||||| ||||| |||||||| ||||||||||||||||||||||  ||||   | || ||||| |   |||| || || |  |  || |  ||  |   |  | |  ||    | ||   | || |  |    |    | | || | ||  |     | |   |   |   
ATGTTTACTCAACTGCGCTTCACATATGAACAAGAGAGTCATCCAGAGGAGTTTTTTATCCCATATGTCTGGCAGCTAGTTCTATCCCATTGgta-tgattcctggagcttttctattcacattgtct-caaggctacatataattattttactcttacattttgagttgtgttggtcttgttttatttcattc

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|33683149|gb|CF311388.1|CF311388
EST:     CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG                         ATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
genomic: CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgtttt ... gcattaccagATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
EST: gi|88458795|gb|CI558456.1|CI558456
EST:     CTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG                         ATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
genomic: CTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgtttt ... gcattaccagATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
EST: gi|5004229|gb|AU069378.1|AU069378
EST:     CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG                         ATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
genomic: CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgtttt ... gcattaccagATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
EST: gi|89167227|gb|CI104513.1|CI104513
EST:     CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG                         ATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
genomic: CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgtttt ... gcattaccagATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
EST: gi|33800537|gb|CF326139.1|CF326139
EST:     CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG                         ATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
genomic: CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgtttt ... gcattaccagATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
EST: gi|88438333|gb|CI541077.1|CI541077
EST:     CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG                         ATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
genomic: CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgtttt ... gcattaccagATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
EST: gi|12622135|gb|AU172348.1|AU172348
EST:     CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG                         ATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
genomic: CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgtttt ... gcattaccagATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
EST: gi|5004218|gb|AU069367.1|AU069367
EST:     CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG                         ATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
genomic: CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgtttt ... gcattaccagATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
EST: gi|86497820|gb|CI140453.1|CI140453
EST:     CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG                         ATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
genomic: CCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgtttt ... gcattaccagATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
EST: gi|38479720|gb|CF963809.1|CF963809
EST:     AGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGG                         ATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT
genomic: AGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgtttt ... gcattaccagATTCTCTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTTTACCCAGTTACGGTTTACATATGAGCAAGAAAGTCATCCTGAGGAGTTTTTTATCCCATATGCATGGCGCGTTGTCCTATCACGAGGgtaatgttttcctgttctctcttaggcttgtcatgtataaaagaaaatgagaataataaaacagtttggtcttaggtatgcagcgagcgatgactaaaaa

- - - - - - - - - - - - - - - - - - - - - -  GAGGAG