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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactgaaattcggatgtattcatgagcatacccaactacatttataaattgtaatagcaacttattcctatatgttatttttgcacgttctgatttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAG

Basic information

species Oryza sativa
transcript LOC_Os02g47110.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G113995_T01 (Zea mays), 3'ss of exon 3
tactgaaattcggatgtattcatgagcatacccaactacattta-taaattgtaatagcaacttattcctatatgttatttttgcacgttctgatttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAG
|       ||  |||    |  | |   | |  |  |   ||   |  ||  | ||  | | |||| | |      | ||| ||||||||  || ||| ||||||| ||||||||||| |||||| | |||||||| |||||||| ||||| || ||||||
tttcttccttgagataacattttaaat-tccagagttttgttgggtttatgattatgaccagttatacatggtaactctttatgcacgtttcgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 3
-tactgaaattcggatgtattcatgagcatacccaactacatttataaatt-gtaatagcaacttattcctatatgttatttttgcacgttctgatttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAG
 | ||    |||      || |     || |  | |     |||     ||  | ||  | ||  || |        | ||| |||| |||| |  |||||||||||||||||||||||||||||| | ||||| || |||||||| ||||| || ||||||
ctgcttttcttcctcaagataccgtttcaaattccagagttttttcgggtttatgattacgac--atacacggtgactctttatgcatgttcggtgttgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG

upper sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 3
--tactgaaattcggatgtattcatgagcatacccaactacatttataaattgtaatagcaacttattcctatatgttatttttgcacgttctg-atttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAG
   |       |  || |||| | ||  |||      || |  ||     || |  || |||   |  |||  |  |   ||    | | |||  || ||||||||||||| |||||||| |||||| ||||||| || |||||||| || || |||||||||
aacatactttcttagaagtat-cttgttcatttttttcttctatt--tggtttttgtaacaatgaagccctcaacctatgttgaaaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG

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|66919065|gb|CX105913.1|CX105913
EST:     AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTG                         ATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCG
genomic: AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttg ... tgatttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCG
EST: gi|2310427|gb|C26582.1|C26582
EST:     AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTG                         ATCTATGTAGTTGATTCATTGGNTAGAGGAGAGAATCGGAAAAGCGAAA-C
genomic: AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttg ... tgatttgcagATCTATGTAGTTGATTCATTGGATAGAG-AGAGAATCGGAAAAGCGAAAGC
EST: gi|88311186|gb|CI570260.1|CI570260
EST:     AGAAGTTGACGCCTCTGTGGAGGCCTTACTTCACTAATACGGATGGTTTG                         ATCTATGTAGTTGATTCATTGGATACAGAGAGAAT-GGAAA-GCGAA
genomic: AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttg ... tgatttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAA
EST: gi|2310382|gb|C26537.1|C26537
EST:     AAGTTGAAGGCCTCTGTTGGAGGCATTACTTCAATAATACGGATGGTTTN                         ATCTATGTAGTTGATTCATT
genomic: AAGTTGA-GGCCTCTGT-GGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttg ... tgatttgcagATCTATGTAGTTGATTCATT
EST: gi|33692402|gb|CF320641.1|CF320641
EST:     AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTG                         ATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCG
genomic: AGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAATAATACGGATGGTTTGgtatgttttg ... tgatttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattgtaatagcaacttattcctatatgttatttttgcacgttctgatttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAG
                                          ttctgat  putative branch site (score: 3)
                ttattcctatatgtta  TA-rich tract