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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgttttcctttagaatctcagtacttcacattctgaatttcaggcctatggatgcctaaattttatcatattttgttgcaaaactcttttgga...

Basic information

species Oryza sativa
transcript LOC_Os03g21914.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21914.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 9
GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgttttcctttagaatct-cag-----tacttcacattctgaatttcaggcctatggatgcctaaattttatcatattttgttgcaaaactcttttgga
|||||||||||||||||||| |||||||| ||||||||||| ||||| || ||||||| ||    | |||   ||    || |||      | |||| || |   ||||  | |||| | |  |    ||    |  || | | || |     |||  ||  
GTTGATGATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCAGgtgattttttcttctaatattgcctacagatgcacatttcatataccacattt--gaccta-gaagacactgatgcagtagtaatctattacgtg-ttctcgtg--

upper sequence: LOC_Os03g21914.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G154716_T01 (Zea mays), 5'ss of exon 11
GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgttttcctttagaatct------cagtacttcacattctgaatttcaggcctatggatgcctaaattttatcatattttgttgcaaaactcttttgga
|||||||||||||||||||| |||||||| ||||||||||| ||||| || |||| || ||    | |||   ||    ||      |   | |||| || |   ||||  | |||| | |  |    ||    |  || | | ||||     |||  ||  
GTTGATGATTACAGCATGGTTAATTTCATTCCACTTGATTTGAGAAAGGAAAGCATgtgattttttcttctaatattgcctacagatccacatttcatataccacattt--gaccta-gaagacactgatgcagtagtaatctattgcgtg-ttctcgtg--
















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|218497501|gb|FG955303.1|FG955303
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGACTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|86259754|gb|CI065627.1|CI065627
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|163929298|gb|EG711035.1|EG711035
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|88516777|gb|CI442433.1|CI442433
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|88239119|gb|CI240281.1|CI240281
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|88481114|gb|CI418385.1|CI418385
EST:     CATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
genomic: CATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|88436774|gb|CI521525.1|CI521525
EST:     GGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
genomic: GGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|27546018|gb|CA764157.2|CA764157
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAGCTGCATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|88296035|gb|CI535198.1|CI535198
EST:     TTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
genomic: TTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|58679583|gb|CK068270.1|CK068270
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAGGTGCATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|33679512|gb|CF307751.1|CF307751
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGACTTAAGAAAAGAGAGCAG                         CATTCAGTATTGTGCTGTCGCACATCGACAACTGCA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTAT-GTGCTGTCGCACATCGACAACTGCA
EST: gi|86886652|gb|CI312537.1|CI312537
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|88509021|gb|CI436527.1|CI436527
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|88459826|gb|CI524285.1|CI524285
EST:     AGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
genomic: AGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|313079574|gb|HO213132.1|HO213132
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAGCTGCATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|58663098|gb|CK051784.1|CK051784
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAGCTGCATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|88257250|gb|CI359638.1|CI359638
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|44673938|gb|CR287372.1|CR287372
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAGCTGCATCCAGTATGGGGAAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|89179770|gb|CI044049.1|CI044049
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGA
EST: gi|8857451|gb|AU094769.1|AU094769
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAG                         CATTCCAGTAAT-NGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTA
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATT-CAGT-ATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTA
EST: gi|218503197|gb|FG958153.1|FG958153
EST:     GATTACAGCATGGTGAATTTCATCCCACTTGATTTACGACAAGAGAGCAA                         CATTCAGTATGTGCTGTCGCACATCGACAGCTGCATCCAGTATGGGG
genomic: GATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGG

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: 44 (upstream exon), 17 (downstream exon)
Score: 4

GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgt ... ctttttccagCATTCAGTATGTGCTGTCGCACATCGACAACTGCATCCAGTATGGGGTAGACGCAGATGTGAAGGTTAGGGACTTCGATCCCGAGGACTAATCATTTGAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATGATTACAGCATGGTGAATTTCATCCCACTTGATTTAAGAAAAGAGAGCAGgtaatgccgttttcctttagaatctcagtacttcacattctgaatttcaggcctatggatgcctaaattttatcatattttgttgcaaaactcttttgga

- - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG