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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcgttttcctccgctgcgtctcttcgtttcgaacggttgtggatttcgcttcgacattttgtgttctgacttggttttggtggaaatcgcag

Basic information

species Oryza sativa
transcript LOC_Os09g37910.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g37910.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G162284_T02 (Zea mays), 5'ss of exon 4
GGAGCAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcgttttcctccgctgcgtctcttcgtttcgaacggttgtgg-atttcgcttcgacatt----ttg--tgttctgacttggttttggtggaaatcgcag------------------------------
|||| |||||||||||||||||||||||||||||||||| || || || ||||| |||||||| || ||||    |  |      || | |||||||| | | |||     |  || |  ||||    |||  |||||    || | |    || || |  |                                
GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGTCTCAGTGgtaagtgttgtttcatccatcattccttcattgtttcgaatgttagtgatgcatgactccttcattggatttgaatgttcgtgatttgctgacatgaaacttccgtttctgatgtttgttactttgtggatgtcag

upper sequence: LOC_Os09g37910.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G066528_T02 (Zea mays), 5'ss of exon 4
GGAGCAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcgttttcctccgctgcgtctcttcgtttcgaacggttgtgg-atttcgcttcgacattttgtgttctgacttggttttgg---tggaaatcgcag
|||| |||||||||||||||||||||||||||||||||| || ||||| ||||| |||||||||    |  |||     | ||||  |||| ||||||   | ||||      | |  || ||||    |||||| || || |||    ||  |||  |||
GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAGCAAGTCTCCGTGgtaagctgtttcatccatgatttcgtca-ttcgattcgaatattcgtggcggcctgttatgatatttgcgtttctgattttgtgttgtgtttgtgaatgacag
















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|86256064|gb|CI007780.1|CI007780
EST:     TCAAGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: TCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|33677032|gb|CF305271.1|CF305271
EST:     CAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCCAGGTCTCGGTG                         ATTGACAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: CAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAG-CAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|33677015|gb|CF305254.1|CF305254
EST:     TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|89176361|gb|CI043382.1|CI043382
EST:     TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|66947180|gb|AU312024.1|AU312024
EST:     TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|86527793|gb|CI167999.1|CI167999
EST:     TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|33664894|gb|CF295861.1|CF295861
EST:     CCCCAACGTCAAGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: CCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|88728459|gb|CI751969.1|CI751969
EST:     TCAGGAAGGACTACAAGGAGAACCACCCCAACGTCAAGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|89180836|gb|CI009744.1|CI009744
EST:     CAACGTCAAGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: CAACGTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|86253064|gb|CI057989.1|CI057989
EST:     CAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: CAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|13896450|gb|AU182786.1|AU182786
EST:     AGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: AGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|86517396|gb|CI157602.1|CI157602
EST:     TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|33680144|gb|CF308383.1|CF308383
EST:     CCCAACGTCAAGCAGGTCTCGGTG                         ATTGGTAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: CCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|33656519|gb|CF279133.1|CF279133
EST:     GTCAAGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: GTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
EST: gi|32947912|gb|BP184484.1|BP184484
EST:     TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTG                         ATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT
genomic: TCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 58 (upstream exon), 53 (downstream exon)
Score: 162

GGAGCAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcg ... gaaatcgcagATTGGCAAGGCTGGTGGTGACAAGTGGAAGTCCATGACTGATGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTGgtaagcgtcgttttcctccgctgcgtctcttcgtttcgaacggttgtggatttcgcttcgacattttgtgttctgacttggttttggtggaaatcgcag

- - - - - - - - - - - AAGGAG
- - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - AGAAGC