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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcgacctcctaatccatcctactctataaatgtcataattctcacctgaatataacctgtgtaactaatttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g64660.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G836250_T02 (Zea mays), 3'ss of exon 5
---gtaatcgacc--tcctaatccatcc-tactctataaatgtcataattctcacctgaatataacc----tgtgtaactaatttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG
    ||| | |    | ||  |  | || |  |||   || || || ||    | |  |||||||      || | ||| ||| |||||||||| |||||||| ||||||| |||||||||||||||||| || || || || || |||||||||||| |||| |||||||||||||||
gtaataaccaattaattctcttgaacccatcttctccgaaggtaatcatctgtaacgaaatataattgacatgcgcaaccaatctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCACTTGGGGAGTTCATACTAACCCATCCAGACATCAAG

upper sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 6
---gtaatc--gacctcctaatccatcc----tactctataaatgtcataat---tctcacctgaatataacctg-----tgtaactaatttgat-gcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG
   | | ||  ||| |||   |   ||     |  | ||| ||| |  || |   | |    |   | |  |||      || |    | ||  | |||||||||  | || ||||||| |||||| ||||| || || ||||||||||| || |||||||||||| | ||||| ||| |||| |||
tctgcagtctagacttccatctttttctctggtgttgtattaatttggtactgcatttattttaggtgttgccttaattttgcattacacttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG
















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|29686739|gb|CB683014.1|CB683014
EST:     GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|58588683|gb|CF986991.1|CF986991
EST:     GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|29613014|gb|CB618027.1|CB618027
EST:     GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|29617760|gb|CB622772.1|CB622772
EST:     CTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: CTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|38473796|gb|CF957928.1|CF957928
EST:     NAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|33820806|gb|CF336207.1|CF336207
EST:     G-AAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|27546650|gb|CA764792.2|CA764792
EST:     GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTCGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|29682614|gb|CB678889.1|CB678889
EST:     ATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: ATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT

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: 70 (upstream exon), 72 (downstream exon)
Score: 45

CATGATCAAAGATAAGGAGAATGTGACTCTTGAGGACGTGTTACAGCCTGGAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctataaatgtcataattctcacctgaatataacctgtgtaactaatttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG
                                      taactaattt  TA-rich tract