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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacaacacataaccttgatgacaggctataatttttgttattttattctttttgtacaaatgattctcacctgaaagttttaacacattcctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g27880.1
intron # 7
splice site 3'
intron type U2

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|86845347|gb|CI340425.1|CI340425
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|86494185|gb|CI136818.1|CI136818
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCCCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|88840734|gb|CI080188.1|CI080188
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|86841284|gb|CI342995.1|CI342995
EST:     CTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|88260958|gb|CI364534.1|CI364534
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|33381454|gb|CF196797.1|CF196797
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|86434825|gb|CI106058.1|CI106058
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|88273706|gb|CI394112.1|CI394112
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|88828574|gb|CI073444.1|CI073444
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|86602642|gb|CI357006.1|CI357006
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAATCTTGCACTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|88460240|gb|CI529315.1|CI529315
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|14981070|gb|BI305761.1|BI305761
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|86873762|gb|CI341195.1|CI341195
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|88996482|gb|CI259986.1|CI259986
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
EST: gi|88845547|gb|CI084472.1|CI084472
EST:     GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGGGGCAGAAG                         GTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
genomic: GTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG

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: 61 (upstream exon), 69 (downstream exon)
Score: 18

AAACAAGGGAAAAAATACCGAACATGGGTGGACAGACTATTTGTCTCACAGTCTGGTTCAGACAGTTGGCTGGTCAGATTTGACTTGTGGGAGGCAGAAGgttagtcctt ... cctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctttttgtacaaatgattctcacctgaaagttttaacacattcctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG
                                 ttttaac  putative branch site (score: 18)
                                           ttcctacttt  putative PPT
                             aaagttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacaacacataaccttgatgacaggctataatttttgttattttattctttttgtacaaatgattctcacctgaaagttttaacacattcctactttagGTGATGCGCGGTTGTGCTGTTTGACAAGTCTTGCGCTGAATGTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- -caacaca
- - - - - - - cttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacctga