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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC

Basic information

species Oryza sativa
transcript LOC_Os08g42600.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G016997_T01 (Zea mays), 3'ss of exon 14
-gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
  ||  |     || |||| ||  ||| ||||||||     | | |  | | | ||  | |||        | | |  |||     ||||||||||| || || |||||||| ||||||||||||||||| ||||||||||||||| |||| || |||||| | || ||| | ||  ||||| ||||||
gttagttctgtcttgtttttagc-ttttaagaatttc--gcgatgagttggaagtttatatga-------ctgaattatatcctgccagAAAACAGGAGAAGATCATGTTGATATTATCACTTTCTACAATGAAGTATTTATTCCTGCTGTCAAGCCTTTGTTAGTGGAGGTTGGACCTGGTGCTAGTC

upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G033828_T02 (Zea mays), 3'ss of exon 15
gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatc-----agAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
      | |  ||| | ||    ||||||     || |||    |  | | ||| | || |||||| | | |  ||  || | |||     |||||||||| || ||||| || ||||| ||||||||||||||||||||||| |||||| | || ||  | ||| |||| ||| ||||| ||||  | ||  
------gtaagttcctatcttgttttcaa----cttatataagaattttggaatgagtc-gaaagtctatctgatcaaattgtatcctgccagAAAACAGGAGAAGACCACGTCGACATCATCACTTTCTACAACGAAGTATTCATTCCTGCCGTCAAGTCCTTGTTGGTGGAGGTAGGGCCTGGCGCCAGCG

upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
lower sequence: AT3G12280.2 (Arabidopsis thaliana), 3'ss of exon 14
gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
|||  |  ||  ||||  |  | |    | || ||| | |  |    | |  |  |  || ||  ||||   ||  | |    | |||| || ||||   || ||||||||||| ||||| |||||||| ||| ||||||||||| | || || ||  ||||||| ||||||||  |||  |  |   
gtatatatacactcttaaccttatgctgaaaagtttctttactcgg-tggaga--agactaaatttgtg---acaatgacttgaacagAGAATAGGGCCAGATCATGTTGACATCATCACATTCTACAATGAAATATTTATTCCTGCCGTAAAGCCGCTGCTGGTGGAGCTAGGTCCTGTAAGAAACG

upper sequence: LOC_Os08g42600.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv04s0008g02780.t01 (Vitis vinifera), 3'ss of exon 14
gtaactgcactttcttttcagtgtttcaagaattttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
|||  |   |||  | |  | | | | |    |   || ||||  |   | |||        |||  | |  |||  | | | | |||||||||||| |||| |||||||| |||||||| || ||||| ||| | ||||||||  |||| || ||  || |  | ||| | ||| |||||  | |  
gtatgt-tgcttaatctctattctcttagtgttagcttctgttctatgggaaatct------aagcctttcaactgattttg-aacagAAAACAGGGAAGGAACATGTTGATATTATCACATTTTACAATGAAATTTTTATTCCGGCTGTAAAGCCGCTGTTAATGGAGATTGGGCCTGGTGGTGGAA

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|58675166|gb|CK063853.1|CK063853
EST:     AAGTTTTCCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGG                         AAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTT
genomic: AAGTTTTCCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGGgtaactgcac ... atggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTT
EST: gi|58602114|gb|CK012642.1|CK012642
EST:     AGTTTTCCCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGG                         AAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTT
genomic: AGTTTT-CCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGGgtaactgcac ... atggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTT

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: 47 (upstream exon), 41 (downstream exon)
Score: 4

ATTCAAGGAAATTATTTTCGGCTACAGAAAACAATCTCAGTGCAAGCCACAAGTTTTCCGTAGTGTTTATGTTCATTGGGCATCACGAAGCCGCAATGGGgtaactgcac ... atggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttatgtttaaatcgcaattattctgaaagtgtgtttactcttatggcatcagAAAACAGGGGAGGACCATGTTGACATTATCACTTTCTACAACGAAGTATTTATTCCTACTGTGAAACCTTTGCTGGTTGAGCTAGGGTCTGGTACTAGTC
                                        ctcttat  CT-rich tract
     atgtttaaat  TA-rich tract