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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggccaaaccatcccttaaagcatgttctttggagtcattgtttttctttaggagaaccatcttggtgtcattgttttttttactaactgttactgttctttattataatacggctgtctgcatacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT

Basic information

species Oryza sativa
transcript LOC_Os01g09300.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G147882_T02 (Zea mays), 3'ss of exon 8
gttggccaaaccatcccttaaagcatgttctttggagtcattgtttttctttaggagaaccatcttggtgtcattgttttttttactaactgttactgttctttattataatacggctgtctgcatacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
|| || ||| |   | ||      | | |        |  |  ||  |  |||   |    |||| | |   || || |        ||||| |        ||| ||  | |  | | ||| |  || ||||||||||||||||||||||||||| ||||||| ||||||||  | || 
gtaggacaacctgcctctctgt-tacgatgaacaagtttgtacttagttcttactggg---atctggatcaaatagtgtc-------aactgctttctcatgttagtaacacagtgttttct-cgcacgtgtagGTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCG

upper sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 8
gttggccaaaccatcccttaaagcatgttctttggagtcattgtttttctttaggagaaccatcttggtgtcattgttttttttactaactgttactgttctttattataatacggctgtctgcatacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT------------------------------------------------------
|| || ||| |   | ||      | | |        |  |  ||  |  |||   |    |||| | |   || || |        ||||| |        ||| ||  | |  | | ||| |  || ||||||||||||||||||||||||||| ||||||| ||||||||  | ||                                                       
gtaggacaacctgcctctctgt-tacgatgaacaagtttgtacttagttcttactggg---atctggatcaaatagtgtc-------aactgctttctcatgttagtaacacagtgttttct-cgcacgtgtagGTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGGTAAGTTTCGTAACGTCCGTTCATCTTGAGTTGGTAAACTGCCTTAGCTATGCA
















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|25803965|gb|CA759926.1|CA759926
EST:     ATTGTCAATCTTGGCGATATGCTTGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|29662625|gb|CB658900.1|CB658900
EST:     ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|218497246|gb|FG965662.1|FG965662
EST:     ATTGTCAATCTTGGCGATATGCTTGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|33690519|gb|CF318758.1|CF318758
EST:     ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|29615163|gb|CB620176.1|CB620176
EST:     ATTGTCAATCTTGGCGATATGCTTGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|29615162|gb|CB620175.1|CB620175
EST:     ATTGTCAATCTTGGCGATATGCTTGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|29678794|gb|CB675069.1|CB675069
EST:     ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|29638841|gb|CB643850.1|CB643850
EST:     ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|33683276|gb|CF311515.1|CF311515
EST:     ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAA-CCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|218500447|gb|FG953831.1|FG953831
EST:     ATTGTCAATCTTGGCGATATGCTTGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|33690409|gb|CF318648.1|CF318648
EST:     ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|112785412|gb|EE590632.1|EE590632
EST:     ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|29665424|gb|CB661699.1|CB661699
EST:     ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|29680385|gb|CB676660.1|CB676660
EST:     ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|218481515|gb|FG954235.1|FG954235
EST:     ATTGTCAATCTTGGCGATATGCTTGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|33677763|gb|CF306002.1|CF306002
EST:     ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|218492870|gb|FG955679.1|FG955679
EST:     ATTGTCAATCTTGGCGATATGCTTGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGCA-TGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCG-AGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|29642174|gb|CB647181.1|CB647181
EST:     ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
EST: gi|38471976|gb|CF956107.1|CF956107
EST:     ACTGTATTTTCAG                         GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
genomic: ACTGTATTTTCAGgttggccaaa ... atacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttactaactgttactgttctttattataatacggctgtctgcatacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT
    tactaac  putative branch site (score: 0)
             ttactgttctttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggccaaaccatcccttaaagcatgttctttggagtcattgtttttctttaggagaaccatcttggtgtcattgttttttttactaactgttactgttctttattataatacggctgtctgcatacctgtagGTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA