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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacttgttggtggtttccagcatgtgtttttgttgttcataagaaactatcgcacttaaaacacttgatattgccctgatgttggttaaatctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTCCCCCCAACATTTGTCTCAGAACCTTCCACTCCATCAAATTCATTTGTTG

Basic information

species Oryza sativa
transcript LOC_Os04g23890.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 16
tacttgttggtggtttccagcatgtgtttttgttgttcataagaaactatcg--cactt------aaaacacttgat--attgccctgatgttggttaa--atctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTCCCCCCAACATTTGTCTCAGAACCTTCCACTCCATCAAATTCATTTGTTG---
               || | ||||| |  ||||| | ||| |||   | | |  |||||      ||| |  |   |  ||  || || |    | |||  || |  | |||||||||||  |||| ||||||   |  |||||||| ||  | || | ||| |||||||  ||||| ||||| ||| |||||||||||||||| |||||||   
------------tcctcaatcatgtatgcttgttttccatgagagcttcttgagcactttaatacaaagctataagtcaataaccatgctagctgctaatgatatatttcagGTGATAAAGCATTCTACATCA---AGGCGAAGAAGATCTAAGGAGTATCTGCCCCCAAGTTTTGTTTCAGATCCTGCCACTCCATCAAATTCTTTTGTTGGAA
















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|29685192|gb|CB681467.1|CB681467
EST:     TGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAAGGAAGAAGGTCACAAGAATTTCTC
genomic: TGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|29679663|gb|CB675938.1|CB675938
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|29615866|gb|CB620878.1|CB620878
EST:     ACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAAC---GAAGGTCACAAGAATTTCTC
genomic: ACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|33799059|gb|CF325389.1|CF325389
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|29685421|gb|CB681696.1|CB681696
EST:     TGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|29612811|gb|CB617824.1|CB617824
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAAC---GAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|29630592|gb|CB635601.1|CB635601
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|38470322|gb|CF954453.1|CF954453
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACA-GAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|88306572|gb|CI671324.1|CI671324
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|29619194|gb|CB624206.1|CB624206
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAAC---GAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|88578420|gb|CI687351.1|CI687351
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGAATTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAACAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|29618974|gb|CB623986.1|CB623986
EST:     ACTGACTGATTTTGATCTTTCA-TTTTGNACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAAC---GAAGGTCACAAGAATTTCTC
genomic: ACTGACTGATTTTGATCTTTCATTTTTG-ACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|88580457|gb|CI697388.1|CI697388
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|29684157|gb|CB680432.1|CB680432
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
EST: gi|33381050|gb|CF196393.1|CF196393
EST:     TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCAC                         GTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC
genomic: TTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTC

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), 68 (downstream exon)
Score: 32

ATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATGGGCACATTGTACTGACTGATTTTGATCTTTCATTTTTGACGACTTCAAAACCCCACgtaagttgag ... tctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTCCCCCCAACATTTGTCTCAGAACCTTCCACTCCATCAAATTCATTTGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatcgcacttaaaacacttgatattgccctgatgttggttaaatctcctgcagGTGATAAAAAATTCCACATCATTAAAACGAAGAAGGTCACAAGAATTTCTCCCCCCAACATTTGTCTCAGAACCTTCCACTCCATCAAATTCATTTGTTG
                            ccctgat  putative branch site (score: 32)
                                             tctcctgc  putative PPT
        acttaaaa  TA-rich tract