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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagcatcactttatgctttagagtagaattgtcaaattattgttattttaatgattattatgctctcaacctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG

Basic information

species Oryza sativa
transcript LOC_Os06g33710.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g33710.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G047867_T01 (Zea mays), 3'ss of exon 6
gtaagaagcatcacttta----tgctttagagtagaattgtcaaattattgttattttaatgattattatgctctc-aacctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG
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gtaagaatgatcactctacctatgctcaaaattcaatgtataatagtgtgaatatattttttatgacttttctctccaaactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGTGTCCGACTTCATGTTGGTGATG
















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|33686636|gb|CF314875.1|CF314875
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|29681267|gb|CB677542.1|CB677542
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|29678039|gb|CB674314.1|CB674314
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|29661773|gb|CB658048.1|CB658048
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|58689103|gb|CK077790.1|CK077790
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|29674257|gb|CB670532.1|CB670532
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|38468529|gb|CF952660.1|CF952660
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|58690531|gb|CK079218.1|CK079218
EST:     CTCAGTGGAGAACATCGANTATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAA-TATCTGT-GGATTCAAAGATCCCCGT
genomic: CTCAGTGGAGAACATCGA-TATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
EST: gi|29660327|gb|CB656602.1|CB656602
EST:     CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGAT                         GTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT
genomic: CCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGT

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: 75 (upstream exon), 64 (downstream exon)
Score: 67

GGTTGTCGGAGGTGGTGATGGTGGTGTGCTACGAGAAATAGCCAGACATGCCTCAGTGGAGAACATCGATATATGTGAAATAGACCAGCTAGTTATTGATgtaagaagca ... acctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaattgtcaaattattgttattttaatgattattatgctctcaacctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG
                      ttttaat  putative branch site (score: 67)
     ttgtcaaattattgtt  TA-rich tract