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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaattctactgctttcagttcgatggaaatggagtcctgaatttgggatatttgcgctgatcttaactgtgctgattgatatgtgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGA

Basic information

species Oryza sativa
transcript 13114.m00108
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01014.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G40650.1 (Glycine max), 3'ss of exon 5
--gtatgaattc--tactgctttcagttcgatggaaatggagtcctgaatttgggatatttgcgctgat--cttaactgtg--ctgattgatatg-tgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGA
   |   ||  |  || | ||||   ||  |||  |   |  | |  ||  | | |  ||    ||| |  || |  ||||   ||  || ||   ||||||  ||  || |||||||||||||||||||||||||| | ||||| || |   | || || |  || || || || ||||||||  ||||| |  | || |
aattgacaacccattattccttttccttttatgctacaagtattc-aaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA

upper sequence: LOC_Os03g01014.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G04660.1 (Glycine max), 3'ss of exon 5
---------gtatgaattctactgctttcagttcgatggaaatggagtcctgaatttgggatatttgcgctgatcttaactgtgctgattgatatg-tgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGA
           || | | ||  | ||||   | | |     || |    |   |  |   ||  | | |   | |||   ||   ||  || ||   ||||||  ||  || |||||||||||||||||||||||||  | |||||||| |   | ||||| |  || || || || ||||||||  ||||| |  | || |
cttgataacccattattccttttcctttttatgctacaagtataggaagccagaagtttcattctggtgactaacttg--tgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAGGCATTTGCAGCTGTACTTACTGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA

upper sequence: LOC_Os03g01014.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv02s0012g01220.t01 (Vitis vinifera), 3'ss of exon 5
gtatgaattctactgctttcagttcgatggaaatggagtcctgaatttgggatatttgcgctgatcttaactgtgctgattgatatgtgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGA
||| ||  ||  || | ||   ||||         ||   ||||||||   |||| |    |  | | || | | |  ||||       |||| |||  || ||||||||||||| |||||||| ||  |||||||||| |  ||||| || ||||| || || || ||||||||||||||| |  | || |
gtaagagctc--cttccttggtttcggactgtcatgacaactgaattt---atatct----tactgtgaattcttcaaattg-------tagACTGGAGTGCTGCCTCCATTTGTGCCATTTGCCCAGGCGTTTGCAGCTGTAATCACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAA

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|14980697|gb|BI305375.1|BI305375
EST:     TTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTG                         AGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCC
genomic: TTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTGgtatgaattc ... atatgtgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCC
EST: gi|86906380|gb|CI294503.1|CI294503
EST:     TTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTG                         AGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCC
genomic: TTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTGgtatgaattc ... atatgtgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCC
EST: gi|14980567|gb|BI305245.1|BI305245
EST:     TTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTG                         AGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCC
genomic: TTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTGgtatgaattc ... atatgtgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCC
EST: gi|29668134|gb|CB664409.1|CB664409
EST:     TTCTGAGAGGCACAGAGCTCATGANAGACGCTCGAGGGATTGCATCCCTG                         AGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCC
genomic: TTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTGgtatgaattc ... atatgtgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCC
EST: gi|33679460|gb|CF307699.1|CF307699
EST:     TTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTG                         AGTGGCTTGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCC
genomic: TTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTGgtatgaattc ... atatgtgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCC
EST: gi|58609210|gb|CK037243.1|CK037243
EST:     TTCTGAGAGGCACAGAGCTCATGAAAGACGCGCGAGGGATTGCATCCCTG                         AGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCC
genomic: TTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTGgtatgaattc ... atatgtgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCC

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: 68 (upstream exon), 75 (downstream exon)
Score: 44

GGTGCGTTGGCTGATATTTTTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTGgtatgaattc ... atatgtgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcctgaatttgggatatttgcgctgatcttaactgtgctgattgatatgtgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGA
                                         attgatat  TA-rich tract