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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcgtttcgtggtggcaagtggggccttgtgagagattattagggattagggtttaatcaagggtttattgttatgcttatgagcgctccccggggtttgcagGATTGCGACACCATACAGGCTACCAGTGCTGGGAGGCTACGGCTTTCGAAGCCCAACAAATATTGGGTCGAGAGCTCGCAGAAGAGG

Basic information

species Oryza sativa
transcript LOC_Os01g66730.1
intron # 3
splice site 3'
intron type U2

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|29622358|gb|CB627369.1|CB627369
EST:     TCACCGAGATGACCAACCAGACCATCAAGCTCGGCGCTGGCCTGCGACAG                         GATTGCGACACCATACAGGCTACCAGTGCTGGGAGGCTACGGCTTTCGAAG
genomic: TCACCGAGATGACCAACCAGACCATCAAGCTCGGCGCTGGCCTGCGACAGgtaaatcgtt ... gggtttgcagGATTGCGACACCATACAGGCTACCAGTGCTGGGAGGCTACGGCTTTCGAAG
EST: gi|29289898|gb|CB483512.1|CB483512
EST:     TCACCGAGATGACCAACCAGACCATCAAGCTCGGCGCTGGCCTGCGACAG                         GATTGCGACACCATACAGGCTACCAGTGCTGGGAGGCTACGGCTTTCGAAG
genomic: TCACCGAGATGACCAACCAGACCATCAAGCTCGGCGCTGGCCTGCGACAGgtaaatcgtt ... gggtttgcagGATTGCGACACCATACAGGCTACCAGTGCTGGGAGGCTACGGCTTTCGAAG
EST: gi|88333983|gb|CI645397.1|CI645397
EST:     TCACCGAGATGACCAACCAGACCATCAAGCTCGGCGCTGGCCTGCGACAG                         GATTGCGACACCATACAGGCTACCAGTGCTGGGAGGCTACGGCTT
genomic: TCACCGAGATGACCAACCAGACCATCAAGCTCGGCGCTGGCCTGCGACAGgtaaatcgtt ... gggtttgcagGATTGCGACACCATACAGGCTACCAGTGCTGGGAGGCTACGGCTT
EST: gi|29622394|gb|CB627405.1|CB627405
EST:     TCACCGAGATGACCAACCAGACCATCAAGCTCGGCGCTGGCCTGCGACAG                         GATTGCGACACCATACAGGCTACCAGTGCTGGGAGGCTACGGCTTTCGAAG
genomic: TCACCGAGATGACCAACCAGACCATCAAGCTCGGCGCTGGCCTGCGACAGgtaaatcgtt ... gggtttgcagGATTGCGACACCATACAGGCTACCAGTGCTGGGAGGCTACGGCTTTCGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggtttaatcaagggtttattgttatgcttatgagcgctccccggggtttgcagGATTGCGACACCATACAGGCTACCAGTGCTGGGAGGCTACGGCTTTCGAAGCCCAACAAATATTGGGTCGAGAGCTCGCAGAAGAGG
   gtttaat  putative branch site (score: 4)
                tttattgttat  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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcgtttcgtggtggcaagtggggccttgtgagagattattagggattagggtttaatcaagggtttattgttatgcttatgagcgctccccggggtttgcagGATTGCGACACCATACAGGCTACCAGTGCTGGGAGGCTACGGCTTTCGAAGCCCAACAAATATTGGGTCGAGAGCTCGCAGAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG