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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcacttgttaaacaatttatgttcagtataataatctataatgcatcaatcttttcaaccacatactgcaaaagtttccttattttttactgctatttgccaatag

Basic information

species Oryza sativa
transcript LOC_Os09g33500.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 5
GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgat-cacttgttaaacaatttatgttcagtataataatctataatgcatcaatcttttcaaccacatactgcaaaagtttccttattttttactgctatttgccaatag
|| ||||| ||| ||||||| |||||||||||||||||||| || || ||  || ||  | ||  |||| |     | |  ||    |||| |  |||    ||| || |           ||||| ||||   |  ||||||   | ||
GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcattttgtagacgttatagtttcacttgttcagt--atggc-catctacttttct--ccatatgccatctgtagcaccttacttttggttcatatttgttgacag

upper sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 11
GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcacttgt-taaacaatttatgttcagtataataatctataatgcatcaatcttttcaaccacatactgcaaaagtttccttattttttactgctatttgccaatag
|| ||||| ||| ||||||| |||||||||||||||||||| ||  ||| | || |   | ||  ||||||     | |  |||   |||| |  ||||   ||| || |         | ||||| ||||   |  ||||||   | ||
GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattccttttgtagatgttatactttcagttgttcagt--atagc-catctagttttt---ccatatgccatctgtagtaccttacttttggttcatatttgttgacag
















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|86600093|gb|CI258433.1|CI258433
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|88266210|gb|CI377112.1|CI377112
EST:     AAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: AAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|88241310|gb|CI241159.1|CI241159
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|87008136|gb|CI299104.1|CI299104
EST:     TATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: TATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|88201857|gb|CI202212.1|CI202212
EST:     TATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: TATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|87032949|gb|CI187573.1|CI187573
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTT
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTT
EST: gi|88978398|gb|CI384780.1|CI384780
EST:     GAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|86895800|gb|CI316034.1|CI316034
EST:     CAGGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: CAGGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|88219808|gb|CI219368.1|CI219368
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|66929259|gb|CX116107.1|CX116107
EST:     CAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: CAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|86536670|gb|CI176876.1|CI176876
EST:     TCAGGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: TCAGGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|86494245|gb|CI136878.1|CI136878
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|29637529|gb|CB642538.1|CB642538
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|33800162|gb|CF325945.1|CF325945
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|2796459|gb|AA749753.1|AA749753
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAAC-TTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|33380822|gb|CF196165.1|CF196165
EST:     NCCGCAGATATATTGTCCAAAGNNNNAATCAGTGCTGNN                         NTGATAAACCTTCGTTCAATT
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATT
EST: gi|86844834|gb|CI338720.1|CI338720
EST:     GCCGCAGATATATTGTCCAAATAAGGAATCAGGGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCGACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|33666827|gb|CF297794.1|CF297794
EST:     TCAGGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: TCAGGCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|88408234|gb|CI551363.1|CI551363
EST:     TCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: TCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|86542747|gb|CI182953.1|CI182953
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|157649975|gb|EX449609.1|EX449609
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|88218592|gb|CI218441.1|CI218441
EST:     AGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: AGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|87022122|gb|CI259194.1|CI259194
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|88828484|gb|CI073354.1|CI073354
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|2312022|gb|C28177.1|C28177
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|29645720|gb|CB650727.1|CB650727
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|89169219|gb|CI038726.1|CI038726
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|87034409|gb|CI189033.1|CI189033
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|33666828|gb|CF297795.1|CF297795
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|29657623|gb|CB653898.1|CB653898
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
EST: gi|86497317|gb|CI139950.1|CI139950
EST:     GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAG                         GTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA
genomic: GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCA

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: 39 (upstream exon), 72 (downstream exon)
Score: 160

GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcactt ... ttgccaatagGTGATAAACCTTCGTTCAATTAGACCACTTGATAGAGCTACTATCAATGCATCTGTTAGAAAAACAAATAGATTGGTGACCATTGAGGAAAGCTTCCCAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcacttgttaaacaatttatgttcagtataataatctataatgcatcaatcttttcaaccacatactgcaaaagtttccttattttttactgctatttgccaatag

-  GCAGAT
- - - - - - - - - AAAGAA
- - - - - - - - -  AAGAAG
- - - - - - - - - - - AAGGAA