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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgcaaactttggaacatcttatccttggtgaagattaatatctatatgttgataaaatgtctttatttttgttggaaaaagaatgtctattgacagggttgctttcttatgtgcagGCTCCAGTGCTGATAAAATATCCCGCGAGCTTATCCTTAACAGCTTACTCTTATTCATTTGCCACTGTATTCATGGTGCTGACAGGGGTAGTTACAACCA

Basic information

species Oryza sativa
transcript LOC_Os06g49500.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49500.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G134930_T03 (Zea mays), 3'ss of exon 3
-------------------------------------------gtgatgcaaactttggaacatcttatcc-ttggtga-agattaatatctatatgttgataaaatgtctttatttttgttggaaaaagaatgtctattg--acagggttgctttctt---------------atgtgcagGCTCCAGTGCTGATAAAATATCCCGCGAGCTTATCCTTAACAGCTTACTCTTATTCATTTGCCACTGTATTCATGGTGCTGACAGGGGTAGTTACAACCA
                                           |  ||  |    ||| ||  || | ||  ||  |||  ||||  |   |   |  |  |  |||    || |  |   |   |     | | ||  ||  |||   | ||  || |               |  ||||||| || |||||||| ||||| ||||||||||||||| | || || ||||| || || || || ||  | ||||||||| | || || |   |  | ||||
gtgacgcagacttggtgacgcagacttggcagcactggggttggatatatatttattgaaatttcctttctgttactgatggattggtggatgcttactactgtaatcgtattttaatatctacgatgttcacgcctgatgcaacaaaatcgccgtccttttcctgacgcgacaacctgcagGCCCCGGTGCTGATCAAATACCCCGCGAGCTTATCCCTGACCGCCTACTCCTACTCCTTCGCAACCTTGTTCATGGTGGTCACCGGCGCGTTCGCCACCA
















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|218487115|gb|FG960498.1|FG960498
EST:     TGGTCATACAG                         GCT-CAGTGCTGATAAAATATCCCGCGAGCTTATCCTTAACAGCTTACTCT
genomic: TGGTCATACAGgtgatgcaaa ... ttatgtgcagGCTCCAGTGCTGATAAAATATCCCGCGAGCTTATCCTTAACAGCTTACTCT
EST: gi|33682871|gb|CF311110.1|CF311110
EST:     TCTGCCTCATTGGGAACTGCTTCCTGATGGGCGCTTATCTGGTCATACAG                         GCTCCAGTGCTGATAAAATATCCCGCGAGCTTATCCTTAACAGCTTACTCT
genomic: TCTGCCTCATTGGGAACTGCTTCCTGATGGGCGCTTATCTGGTCATACAGgtgatgcaaa ... ttatgtgcagGCTCCAGTGCTGATAAAATATCCCGCGAGCTTATCCTTAACAGCTTACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatttttgttggaaaaagaatgtctattgacagggttgctttcttatgtgcagGCTCCAGTGCTGATAAAATATCCCGCGAGCTTATCCTTAACAGCTTACTCTTATTCATTTGCCACTGTATTCATGGTGCTGACAGGGGTAGTTACAACCA
                          tattgac  putative branch site (score: 2)
                                     ttgctttctt  putative PPT
              aaaaagaat  TA-rich tract