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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcttcagaacaatattcttttggatactgactgtcaaagttatcccaaagttctgaacaattcttttgtggcacttttataacatttctgaactttgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACGATTCAGAGAGGAAGGCCTGGCTTATCCTAGCGTGGGTCAGCACCGTTGC

Basic information

species Oryza sativa
transcript LOC_Os03g05390.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05390.12 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G028521_T01 (Zea mays), 3'ss of exon 3
gtaaatcttcagaacaatattcttttggatactgactgtcaa-agttatcccaaagttctgaacaattcttttgtggcacttttataacatttctgaactttgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACGATTCAGAGAGGAAGGCCTGGCTTATCCTAGCGTGGGTCAGCACCGTTGC
     || |  || | || ||      | |   ||  || |  | ||||       |||||  ||  || |  ||   | |||| |    |  |||   ||| |  |||||| ||| ||||||| |||||||||||||||||||| ||| | || ||||| | |||||||||||| |||||||| ||||| || |||||||||||||| ||
----ttcgtttgatccatgtttcagaagtttgggagagtaattaattattggttcattctgtcca--tcctacgtctgattttttt--tctcactg---ttttttattcagTCCTATTGCTCGGTACAAGAGTGGCTGCATCAGCGGCTTCGATTTCTCATGGTTCAGAGAGGAAAGCCTGGCTCATCCTTGCATGGGTCAGCACCGTGGC
















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|58686588|gb|CK075275.1|CK075275
EST:     TGCTGTGGTGATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAG                         TACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
genomic: TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
EST: gi|29656826|gb|CB653101.1|CB653101
EST:     TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAG                         TACTACTGCTCGGC
genomic: TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGC
EST: gi|88689068|gb|CI732644.1|CI732644
EST:     TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAG                         TACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
genomic: TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
EST: gi|25798436|gb|CA754397.1|CA754397
EST:     TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCCC-G                         TACTACTGCTCGGCACAAGAGTGGCTGCTTCACCTGCTGCAATCTCTCACG
genomic: TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
EST: gi|88985311|gb|CI002828.1|CI002828
EST:     TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAG                         TACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
genomic: TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
EST: gi|29629817|gb|CB634826.1|CB634826
EST:     TGCTGTGGTGATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAG                         TACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
genomic: TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
EST: gi|38478400|gb|CF962533.1|CF962533
EST:     GCGTGTGGTGATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAG                         TACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
genomic: GC-TGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
EST: gi|286636|gb|D15443.1|D15443
EST:     TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAG                         TACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
genomic: TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
EST: gi|218490860|gb|FG966651.1|FG966651
EST:     TGCTGTGGTGATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAG                         TACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
genomic: TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
EST: gi|88974168|gb|CI002787.1|CI002787
EST:     TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAG                         TACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
genomic: TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
EST: gi|2310675|gb|C26830.1|C26830
EST:     TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAG                         TACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
genomic: TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
EST: gi|218481056|gb|FG966658.1|FG966658
EST:     TGCTGTGGTGATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAG                         TACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG
genomic: TGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACG

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: 74 (upstream exon), 75 (downstream exon)
Score: 68

CTCGTTGAACCGTATTCACGAATTGACAGTGCTAAGGGTGTTGCTCTTCTTGCTGTGGTAATTCTTATCCTCTCAAATGTGGCCTCAAATGTTCCCACAGgtaaatcttc ... tgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACGATTCAGAGAGGAAGGCCTGGCTTATCCTAGCGTGGGTCAGCACCGTTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgaacaattcttttgtggcacttttataacatttctgaactttgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACGATTCAGAGAGGAAGGCCTGGCTTATCCTAGCGTGGGTCAGCACCGTTGC
                          ttataac  putative branch site (score: 68)
                                          ctttgtctttc  putative PPT
                      acttttataacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcttcagaacaatattcttttggatactgactgtcaaagttatcccaaagttctgaacaattcttttgtggcacttttataacatttctgaactttgtctttcagTACTACTGCTCGGCACAAGAGTGGCTGCATCAGCTGCTGCAATCTCTCACGATTCAGAGAGGAAGGCCTGGCTTATCCTAGCGTGGGTCAGCACCGTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA