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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctttgacatatacttacaattgacttgtcattaatacccatcaagttatcagctagacatgctctaatcattgttttatattccgaatgagttcagGCACACGCAGCTTCTGCGATTCTAAACTTCAGCGAAAACTGCAGGCCTGATATTTTGACACCATACTTGGATGGGATAGTTGGGAAACTACTGTCATTGC

Basic information

species Oryza sativa
transcript LOC_Os03g49420.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 1
---ttttctttga--catatacttacaat--tgacttgtcattaatacccatcaagttatcagctagacatgctctaatcattgttttatattccgaatgagttcagGCACACGCAGCTTCTGCGATTCTAAACTTCAGCGAAAACTGCAGGCCTGATATTTTGACACCATACTTGGATGGGATAGTTGGGAAACTACTGTCATTGC
   ||| | |  |  |     ||| | ||     ||  |||| || || || ||  | | ||   || ||| |||| |    | |||||| | |   |||  |||||||||| || || || || ||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||  |||||||||||||| || |  || |
tggtttacataaagtcgagggcttgctatatctgctcttcatcaa-acacaccagctgaccaataaggcattctctca----tattttatttcctacatg--ttcagGCACATGCTGCATCAGCTATTCTGAACTTCAGTGAAAACTGCAGACCTGATATTTTGACACCATACTTGGATGTAATAGTTGGGAAACTTCTATTGTTAC

upper sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 4
ttttctttgacatatacttacaattgacttgtcattaatacccatcaagttatc--agctagacatgctcta----atcattgttttatattccgaatgagttcagGCACACGCAGCTTCTGCGATTCTAAACTTCAGCGAAAACTGCAGGCCTGATATTTTGACACCATACTTGGATGGGATAGTTGGGAAACTACTGTCATTGC
    || |    |||| | |  || || || | ||| | |  | ||  | |||   |  || | | ||| |      | ||| || |  |       |     |||||||| || ||||| ||  |||| ||||||||||| |||||||  |||||||| || || ||||||||||||||||||||| | ||||||||   | | |
----ctattctttatagtcattat-gatttataattga-agtcgtcttgctattttaattaaataagctatctggtgtaattattctcaaaatattgtctacacagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGGATAGTTAGCAAACTACTTGTACTTC

upper sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 2
ttttctttgacatatacttacaattgacttgtcattaatacccatcaagtta--tcagctagacatgctctaatcattgttttatattccgaatgagttcagGCACACGCAGCTTCTGCGATTCTAAACTTCAGCGAAAACTGCAGGCCTGATATTTTGACACCATACTTGGATGGGATAGTTGGGAAACTACTGTCATTGC
  || | |    | || | |  || || || | ||| |   |   | | |||  | |  ||  | | || |  | ||| ||||  |       |     |||||||| || ||||| ||  |||| ||||||||||| |||||||  |||||||| || || |||||||||||||| |||||| | ||||||||   | | |
-cttttattctttgtagtcattat-gatttatgattgaagtcatgctatttaaattaaataagctttctattgtaattattttcaaaatattgtctacacagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGAATAGTTAGCAAACTACTTGTACTTC

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|29679231|gb|CB675506.1|CB675506
EST:     TGCCTGCATTGGCTTCATCCATGGATGATTTCCAGAACCCGCGCGTACAG                         GCACACGCAGCTTCTGCGATTCTAAACTTCAGCGAAAACTGCAGGCCTGAT
genomic: TGCCTGCATTGGCTTCATCCATGGATGATTTCCAGAACCCGCGCGTACAGgcaagttatt ... atgagttcagGCACACGCAGCTTCTGCGATTCTAAACTTCAGCGAAAACTGCAGGCCTGAT
EST: gi|571970|gb|D41481.1|D41481
EST:     TGCCTGCATTGGCTTCATCCATGGATGATTTCCAGAACCCGCGCGTACAG                         GCACACGCAGCTTCTGCGATTCTAAACTTCAGCGAAAACTGCAGGCCTGAT
genomic: TGCCTGCATTGGCTTCATCCATGGATGATTTCCAGAACCCGCGCGTACAGgcaagttatt ... atgagttcagGCACACGCAGCTTCTGCGATTCTAAACTTCAGCGAAAACTGCAGGCCTGAT
EST: gi|569698|gb|D40547.1|D40547
EST:     TGCCTGCATTGGCTTCATCCATGGATGATTTCCAGAACCCGCGCGTACAG                         GCACACGCAGCTTCTG-GANTTCTAAACTTCAGCGAAAACTGCAGGCCTGA
genomic: TGCCTGCATTGGCTTCATCCATGGATGATTTCCAGAACCCGCGCGTACAGgcaagttatt ... atgagttcagGCACACGCAGCTTCTGCGA-TTCTAAACTTCAGCGAAAACTGCAGGCCTGA
EST: gi|29629840|gb|CB634849.1|CB634849
EST:     TGCCTGCATTGGCTTCATCCATGGATGATTTCCAGAACCCGCGCGTACAG                         GCACACGCAGCTTCTGCGATTCTAAACTTCAGCGAAAACTGCAGGCCTGAT
genomic: TGCCTGCATTGGCTTCATCCATGGATGATTTCCAGAACCCGCGCGTACAGgcaagttatt ... atgagttcagGCACACGCAGCTTCTGCGATTCTAAACTTCAGCGAAAACTGCAGGCCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagttatcagctagacatgctctaatcattgttttatattccgaatgagttcagGCACACGCAGCTTCTGCGATTCTAAACTTCAGCGAAAACTGCAGGCCTGATATTTTGACACCATACTTGGATGGGATAGTTGGGAAACTACTGTCATTGC
                    ctctaat  putative branch site (score: 3)
                       taatcattgttttata  TA-rich tract