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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAATGATGATGCACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgctccccatcttttaatggattcctgatgcttatcttgaactgatgcatataaacatgcattacatagcacaggttcctgaatacaaaagaaa...

Basic information

species Oryza sativa
transcript LOC_Os09g32220.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G014313_T02 (Zea mays), 5'ss of exon 7
CTAATGATGATGCACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgctccccatcttttaatggattcctgatgcttatcttgaactgatgcatataaaca-----tgcattacatagcacaggttcctgaatacaaaagaaa
| | |||||||||||| ||||||||||| |||||||| ||||||||   ||| || ||||||||| |||||||    | |||||    |||| || ||||| |  |  | |||| |||    |       | ||  |||   |||    |  || || | ||     
CAACTGATGATGCACAGAAGATGATGCAAATGGGTGGTGGATTTGGATTTAACCCAACAATGgtaaggtgctctatgttttttatgcaattcttggtgcttgttcttgattgatacatgatgatgcattgtacaccacacgacactcacttttggattcgaa-----
















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|88834677|gb|CI077960.1|CI077960
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|86511384|gb|CI154017.1|CI154017
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|89195920|gb|CI007339.1|CI007339
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAAGCCTGGATATAATCCAGCATGACTGGGC
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAA-CCTGGATATAATCCAGCATGACTGGGC
EST: gi|86525680|gb|CI165886.1|CI165886
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|66920739|gb|CX107587.1|CX107587
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|86834746|gb|CI340863.1|CI340863
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88525714|gb|CI452740.1|CI452740
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88206181|gb|CI206030.1|CI206030
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88214287|gb|CI214136.1|CI214136
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88255123|gb|CI353947.1|CI353947
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|87032311|gb|CI264092.1|CI264092
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88527605|gb|CI455778.1|CI455778
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|87017018|gb|CI286154.1|CI286154
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|25806351|gb|CA762312.1|CA762312
EST:     CCCAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGGCTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|86523056|gb|CI163262.1|CI163262
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|4716728|gb|AU057844.1|AU057844
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88852557|gb|CI374325.1|CI374325
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GTTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|86528191|gb|CI168397.1|CI168397
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|86506491|gb|CI149124.1|CI149124
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|86854905|gb|CI260973.1|CI260973
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|86545313|gb|CI185519.1|CI185519
EST:     CACTAAAGATGATGCAGATGGTTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGTCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|86836282|gb|CI348237.1|CI348237
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88829310|gb|CI074180.1|CI074180
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|86543296|gb|CI183502.1|CI183502
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88270574|gb|CI385832.1|CI385832
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGCCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88535695|gb|CI462510.1|CI462510
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88530593|gb|CI458999.1|CI458999
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|86417257|gb|CI031466.1|CI031466
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88541386|gb|CI470655.1|CI470655
EST:     CAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|86523141|gb|CI163347.1|CI163347
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88215049|gb|CI214898.1|CI214898
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGTCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|13895966|gb|AU182302.1|AU182302
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88252682|gb|CI351110.1|CI351110
EST:     CACAAAAGATGATCCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|33665107|gb|CF296074.1|CF296074
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|88901768|gb|CI374376.1|CI374376
EST:     CACAAAAGATGATGCAGATGGTTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|33688253|gb|CF316492.1|CF316492
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
EST: gi|86251662|gb|CI016951.1|CI016951
EST:     CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATG                         GGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT
genomic: CACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCT

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: 62 (upstream exon), 74 (downstream exon)
Score: 52

CTAATGATGATGCACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgct ... ctgtttccagGGTTTGGCCGCAGAGAAAGACAACCTGGATATAATCCAGCATGACTGGGCTTTACCAAAGATGGAGCATCATGCTGAGGAAGTGCTGAGGAAGCTTCTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAATGATGATGCACAAAAGATGATGCAGATGGGTGGGGGATTTGGCGGTAATCCCACAATGgtatggtgctccccatcttttaatggattcctgatgcttatcttgaactgatgcatataaacatgcattacatagcacaggttcctgaatacaaaagaaa

- - - - - - - -  AAGATG
- - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa