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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttattttctctgcatccaatttgtgataaaatgtttatctgcacatttctgtcatgattagtttgctgcaccttacatttcctatgctaaaaactcagGGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGCTATGCATCTACGGATGGAAGAAGCTGTAAGCCCTTCAATCCACTTCTTG

Basic information

species Oryza sativa
transcript LOC_Os03g49770.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49770.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147332_T01 (Zea mays), 3'ss of exon 4
atttattttctctgcatccaatttgtgataaaatgtttatctgcacatttctgtcatgattagtttgctgcaccttacatttcc----tatgctaaaaactcagGGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGCTATGCATCTACGGATGGAAGAAGCTGTAAGCCCTTCAATCCACTTCTTG
  |   |  |  |   |   ||      | ||||  ||| ||          ||  | ||| |  | |  || || |  | ||     | || |  | ||  |||| |||||||| |||||||| ||||| ||||||||||||||||||||||| ||||| ||||| ||||| || ||||||||||| || || || |||||||
-ctcgctcccgttatctgtgat---aactgaaatagttagctagtggaaaaggtgcttatttgcattcaacagctcatgtatctgatttgtgttttatacctagGGGAATAGTCTTATGAGGATTCTTAGCGTAGCAGCATTTGCTGTTTCTGGATATGCCTCTACAGATGGCAGGAGCTGTAAGCCTTTTAACCCCCTTCTTG

upper sequence: LOC_Os03g49770.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G157172_T01 (Zea mays), 3'ss of exon 5
atttattttctctgcatccaatttgtgataaa-atgtttatctgcacatttctg----tcatgattagtttgctgcaccttacatttcctatgctaaaaactcagGGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGCTATGCATCTACGGATGGAAGAAGCTGTAAGCCCTTCAATCCACTTCTTG
    ||         | | || | || | ||| ||| |||| |||  ||   ||    |  | |    |  || || |  ||| | |  | || |    ||| |||| |||||||| |||||||| |||||  |||||||||||||||||||||| ||||| ||||| ||||| || ||||||||||| || ||||| |||||||
----ataactggaatagctaactagtaaaaaagatgcttatttgctaatgaatgaggctggtcacagttaagcagctcactacctgttttgtgttttgtact-agGGGAATAGTCTTATGAGGATTCTTAGCATAGCAGCATTTGCTGTTTCTGGATATGCCTCTACAGATGGGAGGAGCTGTAAGCCTTTTAATCCCCTTCTTG

upper sequence: LOC_Os03g49770.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 4
atttattttctctgcatccaatttgtgataaaatgtttatctgcacatttctgtcatgattagtttgctgcaccttacatt-tcctatgctaaaaa-ctcagGGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGCTATGCATCTACGGATGGAAGAAGCTGTAAGCCCTTCAATCCACTTCTTG
     ||||     ||  | | |  | |    || |   |  |    |   | |   | ||   |||||  |||    ||| | ||    | ||   ||||||| |||||||| ||||||||  | | |||||| ||||||||||||||||| || || ||||| || |||||||  || || || || |||||| | || |
--cagttttagagccagtctaatcataagtttatttggttgagttagtcctttttcagtttgacttgcttaacccctaattcttctgaattgaacctctcagGGAAATAGTCTAATGAGGATTTTGAATGTAGCTGCATTTGCTGTTTCTGGATACGCTTCTACCGAAGGAAGAACATGCAAACCATTTAATCCATTACTAG

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|29682317|gb|CB678592.1|CB678592
EST:     ATCTTGAGTATTCCTACCTTATTGATCGCGCTTATGAATGGGGGAAAAGG                         GGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGC
genomic: ATCTTGAGTATTCCTACCTTATTGATCGCGCTTATGAATGGGGGAAAAGGgtatttcttc ... aaaaactcagGGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGC
EST: gi|27546683|gb|CA764876.2|CA764876
EST:     ATCTTGAGTATTCCTACCTTATTGATCGCGCTTACGAATGGGGGAAAAGG                         GGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGC
genomic: ATCTTGAGTATTCCTACCTTATTGATCGCGCTTATGAATGGGGGAAAAGGgtatttcttc ... aaaaactcagGGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGC
EST: gi|66924363|gb|CX111211.1|CX111211
EST:     ATCTTGAGTATTCCTACCTTATTGATCGCGCTTATGAATGGGGGAAAAGG                         GGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGC
genomic: ATCTTGAGTATTCCTACCTTATTGATCGCGCTTATGAATGGGGGAAAAGGgtatttcttc ... aaaaactcagGGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGC
EST: gi|163927376|gb|EG709904.1|EG709904
EST:     GCTTATGAATGGGGGAAAAGG                         GGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGC
genomic: GCTTATGAATGGGGGAAAAGGgtatttcttc ... aaaaactcagGGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttctgtcatgattagtttgctgcaccttacatttcctatgctaaaaactcagGGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGCTATGCATCTACGGATGGAAGAAGCTGTAAGCCCTTCAATCCACTTCTTG
                                         tgctaaa  putative branch site (score: 2)
             attagttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttattttctctgcatccaatttgtgataaaatgtttatctgcacatttctgtcatgattagtttgctgcaccttacatttcctatgctaaaaactcagGGCAATAGTCTGATGAGGATCCTTAGTGTAGCAGCATTTGCTGTTTCTGGCTATGCATCTACGGATGGAAGAAGCTGTAAGCCCTTCAATCCACTTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG