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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtttcaatctaggctgaaaaaaagggtgaaattatcacatgtctgtctagcgtttgtttaactcagttggggttccggcgctgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGAGGTGATCAATGGGAATTGGGATGAGGTTGAGCGCTACCTCGGTGGCTTT

Basic information

species Oryza sativa
transcript LOC_Os03g14980.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G030422_T01 (Zea mays), 3'ss of exon 2
gtgagtg-tttcaatctaggctgaaaaaaagggtgaaattatcacatgtctgtctagcgtttgtttaactcagttggggttccggcgctgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGAGGTGATCAATGGGAATTGGGATGAGGTTGAGCGCTACCTCGGTGGCTTT
||||||| ||| |||| | | ||||||      || | || ||    |  ||||||     | | |  ||||||||  | |||   | || |||||||||| ||||||||||| || ||||| |||||||| |||||||| || ||||| ||  |||||||||||||||||||||| ||||||||||| ||||| || 
gtgagtgatttgaatcaaaggtgaaaa------tggacttgtctttag--tgtcta-----tttcttgctcagttgtcgctcc--tgttgctgttcagGCTCGAGCAGGAGTCCGGATTCTATTTCAACATAAAGTACTTTGAGGACGAAGTCCTCAATGGGAATTGGGATGAGGTGGAGCGCTACCTTGGTGGATTC

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ37833 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtgtttcaatctaggctgaaaaaaagggtgaaattatcacatgtctgtctagcgtttgtttaactcagttggggttccggcgctgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGAGGTGATCAATGGGAATTGGGATGAGGTTGAGCGCTACCTCGGTGGCTTT
                                     | |  | || | ||  | |   |||||       ||  | |||  |    | | |  |||||| ||||| || ||||| ||||||||||||||||||||||| |||||  ||||    |||||| | ||||| ||||| ||| | ||| |   |||||| 
------------------------------------gtgagaagatttgtggtttgttcttgttggtggatgtaagtgttgtgtgattttgg--cagGCTGGAGCAAGAATCTGGCTTCTACTTCAACATGAAGTACTTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtgtttcaatctaggctgaaaaaaagggtgaaattatcacatgtctgtctagcgtttgtttaactcagttggggttccggcgctgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGAGGTGATCAATGGGAATTGGGATGAGGTTGAGCGCTACCTCGGTGGCTTT
                                     | |  | || | ||  | |   |||||       ||  | |||  | || | |||  |||||| ||||| || ||||| ||||||||||||||||||||||| |||||  ||||    |||||| | ||||| ||||| ||| | ||| |   |||||| 
------------------------------------gtgagaagatttgtggtttgttcttgttggtggatgtaagtgttgtg-cgattttgg-cagGCTGGAGCAAGAATCTGGCTTCTACTTCAACATGAAGTACTTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC

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|88361379|gb|CI626483.1|CI626483
EST:     CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAA                         GCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
genomic: CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
EST: gi|88352344|gb|CI615598.1|CI615598
EST:     CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAA                         GCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
genomic: CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
EST: gi|29629469|gb|CB634478.1|CB634478
EST:     CTCATCCTCCTTTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAA                         GCTTGAGCAGGAGTCTGGGTTCTACTTCAACATCAAGTACTTCGAAGACGA
genomic: CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
EST: gi|88730409|gb|CI754022.1|CI754022
EST:     CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAA                         GCTTGACCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAACACGA
genomic: CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
EST: gi|88337088|gb|CI628174.1|CI628174
EST:     CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAA                         GCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
genomic: CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
EST: gi|88724837|gb|CI748096.1|CI748096
EST:     CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAA                         GCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
genomic: CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
EST: gi|88298806|gb|CI566003.1|CI566003
EST:     CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAA                         GCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
genomic: CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
EST: gi|58662919|gb|CK051605.1|CK051605
EST:     CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAA                         GCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
genomic: CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
EST: gi|88343434|gb|CI621802.1|CI621802
EST:     CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAA                         GCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTAATTCGAAGACGA
genomic: CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
EST: gi|88719564|gb|CI743074.1|CI743074
EST:     CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAA                         GCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
genomic: CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
EST: gi|58652923|gb|CK041603.1|CK041603
EST:     CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAA                         GCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
genomic: CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
EST: gi|88412321|gb|CI573597.1|CI573597
EST:     CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAA                         GCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA
genomic: CTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGA

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), 74 (downstream exon)
Score: 85

GTGCGGCGGTGGAGGGGAGGATGTCGTCGCTGAGCCGGGAGCTGGTATTCCTCATCCTGCAGTTCCTCGATGAGGAGAAGTTCAAGGAGACTGTTCACAAgtgagtgttt ... tgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGAGGTGATCAATGGGAATTGGGATGAGGTTGAGCGCTACCTCGGTGGCTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtctgtctagcgtttgtttaactcagttggggttccggcgctgttgttcagGCTTGAGCAGGAGTCTGGGTTCTACTTCAACATGAAGTACTTCGAAGACGAGGTGATCAATGGGAATTGGGATGAGGTTGAGCGCTACCTCGGTGGCTTT
                   gtttaac  putative branch site (score: 85)
                tttgtttaa  TA-rich tract