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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttactaatggagctatgatcagattgttgataattagtttttccttcctttcggaatgtggatctggagaaggatcatgatatggttgaattgg...

Basic information

species Oryza sativa
transcript LOC_Os06g36770.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 12
TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttactaatgg----agctatgatcagattgttgataatta-gtttttccttcctttcggaatgtggatctggagaaggatcatgatatggttgaattgg
 ||| | || || ||||||||||||||| | || ||||| || || || |||||||| || |||| |||||||||||||||||| | ||||       ||  ||||||||    |    ||  | | | |    |  |||   |||   |||    | |    | |  | |      |     
CAATCTCTTCCGCGTTTTTGGCTGTACTGCAGGAAGCACCGAGGCTACAACTTTGGAAGCCAGCAAAAACCCCATGAGgtatgtgtcctaactataacagtaatgatcagtgcatgacaaaccatggtatcaagtgatttaacaataatgatgccaatatcagtaacaagaataacaa-----
















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|58655643|gb|CK044323.1|CK044323
EST:     CTGGGAGCGAGGGA-GCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CTGGGAGC-ACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|86483283|gb|CI125916.1|CI125916
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|58675521|gb|CK064208.1|CK064208
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|66913089|gb|CX099937.1|CX099937
EST:     CTGGGAGCACAGAAGCGACCACTTTGGAGGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CTGGGAGCACAGAAGCGACCACTTTGGA-GGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|29630757|gb|CB635766.1|CB635766
EST:     GGAGCACAGAAGCGACCCCTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTTTGGC
genomic: GGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|29627088|gb|CB632099.1|CB632099
EST:     TTTGGGGGCAAGCAGAACCCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCCCACGCACACTAACCTCTCTGGC
genomic: TTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|218501369|gb|FG965487.1|FG965487
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|58658882|gb|CK047562.1|CK047562
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|88411135|gb|CI606354.1|CI606354
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|58593657|gb|CF991965.1|CF991965
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAG
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAG
EST: gi|29683055|gb|CB679330.1|CB679330
EST:     TTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: TTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|58674786|gb|CK063473.1|CK063473
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACA
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACA
EST: gi|29622204|gb|CB627215.1|CB627215
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
EST: gi|29644040|gb|CB649047.1|CB649047
EST:     CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAG                         GCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC
genomic: CCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttac ... ggatacatagGCGTCAGATTGTAAACCCAACAAGGCCCACACGCACACTAACCTCTCTGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCACTTTGGAGGCAAGCAGAAACCCCATGAGgtatgtttactaatggagctatgatcagattgttgataattagtttttccttcctttcggaatgtggatctggagaaggatcatgatatggttgaattgg

- - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG