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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATATCAGCCTGAAGAACAACCAGAAGCTGACACTGATTACAGCCGAGCTCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtgagctttatattacatatttgcattcactatgcaatttttgttcatttaaagcatgtcagatgagttacatacttatgtagcatttgttaa...

Basic information

species Oryza sativa
transcript LOC_Os01g07760.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07760.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G054559_T01 (Zea mays), 5'ss of exon 3
GAATATCAGCCTGAAGAACAACCAGAAGCTGACACTGATTACAGCCGAGCTCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtgagctttatattacatatttgcattcactatgcaatttttgttcatttaaagcatgtcagatgagttacatacttatgtagcatttgttaa--------
|||||| | || || || || |||||| ||||||||||||||| ||| ||||| || ||||||||||| ||||||||||| || |||||||||||||||||||     ||  | |  ||||       |  |||   |||  | | |||  | |||      | | ||| | | ||   |||| ||  || || | |||         
GAATATGAACCAGAGGAGCACCCAGAACCTGACACTGATTACATCCGGGCTCAAGAGGCTAGGAGGTTTATGATCTATGTTCATACCAAAATGATGATAGgtaatctttgcccctcgtattgtgc---tatatttcatattta-tgtttactaattctttaaacg-cagttaaatt---tactgatacagaatatattatgttatatg

upper sequence: LOC_Os01g07760.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G061969_T02 (Zea mays), 5'ss of exon 4
GAATATCAGCCTGAAGAACAACCAGAAGCTGACACTGATTACAGCCGAGCTCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtgagct-ttatattaca-tat-ttgcattcactatgcaatttttgttcatttaaagcatgtcagatgagttacatacttatgtagcatttgttaa
|||||||| ||||| ||||| |||||| ||| ||||||||||| ||| ||||| || ||||||||||| ||||||||||| ||  |||||||||||||||||      ||  |  || || | || ||| || ||||    ||   | || | || |    ||  | ||    | |  || | |  ||| |   || ||||  
GAATATCAACCTGAGGAACACCCAGAACCTGGCACTGATTACATCCGGGCTCAAGAGGCTAGGAGGTTTATGATCTATGTTCATGCCAAAATGATGATAGgttatctctgtccccttgtactgcactatatttcatttttaatatcacttatttttaacgcaattaagtttactaatataga-atatatattttatatgtt--

upper sequence: LOC_Os01g07760.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G15730.1 (Arabidopsis thaliana), 5'ss of exon 3
GAATATCAGCCTGAAGAACAACCAGAAGCTGACACTGATTACAGCCGAGCTCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtgagctttatattacata-tttgcattcactatgcaatttttgttcatttaaagcatgtcagatgagttacatacttatgtagcatttgttaa
|| ||| ||||||  ||  |||||||  | |||||||||||||   | || || |||||  |  | |||||||| || |||||||||||||||||||| ||||       |  |  |    | | |  |||       ||   || | |||| |   | |  ||| |  |||||  | |||   | || ||          
GAGTATGAGCCTGCTGAGAAACCAGACCCCGACACTGATTACATGAGGGCGCAAGAAGCACGCCGTTTCATGATTTACGTCCACACCAAAATGATGATCGgtaagttcacatttcaacggaaaaaaacttgagaagtatacataaatgttgtgc--ctgattcattt--gatgaaatccat---tttgcag----------

upper sequence: LOC_Os01g07760.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G52570.1 (Arabidopsis thaliana), 5'ss of exon 3
GAATATCAGCCTGAAGAACAACCAGAAGCTGACACTGATTACAGCCGAGCTCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtgagctttatattacatatttgcattcactatgcaatttttgttcatttaaagcatgtcagatgagttacatacttatgtagcatttgttaa
|| ||| |||||  |||  |||| ||| | |||||||| || | |||||| || |||||  |  | |||||||||||||| ||||| |||||||||||||||   |||||   ||||||    | |||| |||  | | |  || |||  |  ||   || ||  | |    |  |  | | ||  | ||          
GAGTATGAGCCTTCAGAGAAACCTGAACCGGACACTGACTATATCCGAGCACAAGAAGCACGCCGCTTCATGATCTATGTTCACACTAAAATGATGATAGgt---gagtg--ttttata----acatttacat--aatttataacttt--tcaatactaaccaaatgattcaacatcaaaattttcgcag----------

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|58685596|gb|CK074283.1|CK074283
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|29626348|gb|CB631359.1|CB631359
EST:     AGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: AGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|218487196|gb|FG969108.1|FG969108
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|86830886|gb|CI293845.1|CI293845
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGT
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGT
EST: gi|218487379|gb|FG968040.1|FG968040
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|38473027|gb|CF957159.1|CF957159
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|38476553|gb|CF960686.1|CF960686
EST:     ATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCGTG-GGACATCAACCAGAGGTCG
genomic: ATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTC-TGCAAACATCAACCAGAGGTCG
EST: gi|38474412|gb|CF958544.1|CF958544
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|218489071|gb|FG948414.1|FG948414
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|58679448|gb|CK068135.1|CK068135
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|58682564|gb|CK071251.1|CK071251
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACC
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACC
EST: gi|33794256|gb|CF323018.1|CF323018
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGC
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGC
EST: gi|29621008|gb|CB626019.1|CB626019
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|88269319|gb|CI380617.1|CI380617
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|58612890|gb|CK040602.1|CK040602
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCAAACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCG
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCG
EST: gi|218497667|gb|FG965117.1|FG965117
EST:     TCA-GAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|29616250|gb|CB621262.1|CB621262
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|58590246|gb|CF988554.1|CF988554
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|29626457|gb|CB631468.1|CB631468
EST:     AATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: AATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|88255535|gb|CI354359.1|CI354359
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATTATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|29643707|gb|CB648714.1|CB648714
EST:     GAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: GAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|86825009|gb|CI358190.1|CI358190
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|29677240|gb|CB673515.1|CB673515
EST:     AATGATGATAG                         TTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: AATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA
EST: gi|38476242|gb|CF960375.1|CF960375
EST:     TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAG                         TTGACGATGAGTACATCATCAGCGGTTCTGCAAACATCAACCAGAGGTCGA
genomic: TCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGA

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), 71 (downstream exon)
Score: 22

GAATATCAGCCTGAAGAACAACCAGAAGCTGACACTGATTACAGCCGAGCTCAGGAAGCTAGGAGGTTCATGATCTATGTCCACACCAAAATGATGATAGgtaccgagtg ... ccattttcagTTGACGATGAGTACATCATCATCGGTTCTGCAAACATCAACCAGAGGTCGATGGACGGCGCTAGGGACTCTGAGATCGCCATGGGCGGGTACCAGCCATA




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