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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCTAAGTATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcctctgcatattgatacgtttgcatttgccgtttcctgtggcttactgccagatccagaatctgaccggtgcatgctttatcatcag

Basic information

species Oryza sativa
transcript LOC_Os08g44400.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44400.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G022866_T01 (Zea mays), 5'ss of exon 8
GGTTCTAAGTATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcctctgcatattgatacgttt----gcat-----------ttgccgtttcctgtggcttactgccagatccagaatctgaccggtgcatgctttatcatcag--
||   |   || | | || ||||  | |||||  |||| |||||  |||||||||||||||||||||||||| ||| ||     |  ||    | ||           ||   ||||   |  || || || ||| ||  || |||||  ||   ||| | | |  ||    
GGAAATTCCTACATTGCTTCAAAAGTCCCACCGCAGCCCATAGAGATATGGGCATATGAGgtctgaatcctcagcacatgagctctcttcttagtatacaggtcatggttatggtttatcgcagcatagtgtcagttctggagtctgaatggctgatggtctgttttcgcag
















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|86899723|gb|CI327545.1|CI327545
EST:     CTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: CTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|55408882|gb|CV721258.1|CV721258
EST:     ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|86834825|gb|CI345909.1|CI345909
EST:     TAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: TAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|86872687|gb|CI341897.1|CI341897
EST:     ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|86843061|gb|CI342256.1|CI342256
EST:     CAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: CAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|33821435|gb|CF336529.1|CF336529
EST:     ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|29687876|gb|CB684151.1|CB684151
EST:     ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|58589659|gb|CF987967.1|CF987967
EST:     ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|38478016|gb|CF962149.1|CF962149
EST:     ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|58593409|gb|CF991717.1|CF991717
EST:     ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|27577571|gb|CB000266.1|CB000266
EST:     CAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: CAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|88996530|gb|CI260034.1|CI260034
EST:     ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|27548923|gb|CA767585.2|CA767585
EST:     ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGGGAGACCCTTGTTGAATTAGAGTTG
genomic: ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|12623212|gb|AU173425.1|AU173425
EST:     ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
EST: gi|29685102|gb|CB681377.1|CB681377
EST:     ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAG                         GGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG
genomic: ATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTG

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: 60 (upstream exon), 68 (downstream exon)
Score: 28

GGTTCTAAGTATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcc ... ttatcatcagGGATCTCCTTTCTGTAAAATAGTACGAGAGACCCTTGTTGAATTAGAGTTGCCACACTTGCTACACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTCTAAGTATACTCCTGCAAAGCTTCCACCCGAGCCAATAGAACTATGGGCATATGAGgtctgaatcctctgcatattgatacgtttgcatttgccgtttcctgtggcttactgccagatccagaatctgaccggtgcatgctttatcatcag

- - - - - - - - - GCAAAG