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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaacgactcctgttatttcatctacttttagtatttaaattaattccattttagtaataatcgatgctactatgcaacaattaagtaataatagaataataatctgatgggtgcagGGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCGGAATAGACTGCACAGGGGGCTTCCATCCATCTCTCTCTGCGCTTGTTGA

Basic information

species Oryza sativa
transcript 13114.m00108
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01014.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G005859_T02 (Zea mays), 3'ss of exon 1
gtactaacgactcctgttatttcatctacttttagtatttaaattaattccattttagtaataatcgatgctactatgcaacaattaagtaataatagaataataatctgatgggtgcagGGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCGGAATAGACTGCACAGGGGGCTTCCATCCATCTCTCTCTGCGCTTGTTGA
                                           | |    ||  |    |   ||  |   |   |  |||   |   |   ||||      ||  ||||    |  ||||||| || |  |||||||||||  | ||||||||||||||||| |||||||| ||||||||||| |||||||||||||| |||||| | || || || ||
------------------------------------------gtgaggctcagctatccatgcattcaaatt--caatcaatcctcccg-gctaatctgtcgatg-tctgcactgcacagGGATCTACGGGGCCATGGCACTCGCCGGGAGATTCATATGCCAAATGGCCGGGATAGACTGCACGGGGGGCTTCCATCCGTCTCTCACGGCACTCGTCGA
















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|14980697|gb|BI305375.1|BI305375
EST:     GGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAAGCTCACCTATGGCATTG                         GGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCG
genomic: GGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTGgtactaacga ... atgggtgcagGGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCG
EST: gi|66916796|gb|CX103644.1|CX103644
EST:     GGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTG                         GGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCG
genomic: GGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTGgtactaacga ... atgggtgcagGGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCG
EST: gi|38481179|gb|CF965268.1|CF965268
EST:     GGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTG                         GGATTTAGGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCG
genomic: GGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTGgtactaacga ... atgggtgcagGGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCG
EST: gi|14980567|gb|BI305245.1|BI305245
EST:     GGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTG                         GGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCG
genomic: GGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTGgtactaacga ... atgggtgcagGGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCG
EST: gi|13420795|gb|AU174885.1|AU174885
EST:     GGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTG                         GGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCG
genomic: GGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTGgtactaacga ... atgggtgcagGGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCG
EST: gi|29668134|gb|CB664409.1|CB664409
EST:     GGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTG                         GGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCG
genomic: GGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTGgtactaacga ... atgggtgcagGGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCG

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: 34 (upstream exon), 69 (downstream exon)
Score: 23

ACCGGCGGAGGCGGAGGAGGCGGGGGCTTCGCAGCCCGGGACGCGGAGCTGGCCATGTGGGAGAGGCTGGGAGCGGTTGTCAGGCTCAGCTATGGCATTGgtactaacga ... atgggtgcagGGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCGGAATAGACTGCACAGGGGGCTTCCATCCATCTCTCTCTGCGCTTGTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatgctactatgcaacaattaagtaataatagaataataatctgatgggtgcagGGATTTATGCCGCCATGGCACTTACTGGGAGATTCATATGCCAGATGGCCGGAATAGACTGCACAGGGGGCTTCCATCCATCTCTCTCTGCGCTTGTTGA
                                        atctgat  putative branch site (score: 23)
              aacaattaagtaataa  TA-rich tract