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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCGCCGACCAGGAGCTCGGGATGGCCGAGCGCGCGCTCTCCGCCGCCGGCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcggggggctttcgcttccgccgcgtgcacttgtgtgattggtggctgaaagtttttttgtgttttttttttcgtttgctgcag

Basic information

species Oryza sativa
transcript LOC_Os08g29720.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G059018_T01 (Zea mays), 5'ss of exon 1
GGCCGCCGACCAGGAGCTCGGGATGGCCGAGCGCGCGCTCTCCGCCGCCGGCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcgggg--tcggggggctt--tcgcttccgccgcgtgcacttgtgtgattggtggctgaaagtttttttgtgttt------tttttttcgt-ttgctgcag
||  || ||||||||||||||||||  |||||||||| ||||||| ||||||||||| |||||||| || ||||||||||||||||| || ||||||||||||||    ||||||  ||   |||||  ||| |    | |||    || || ||  ||       ||| | || |      |||  |  || ||| |||||
GGGGGCGGACCAGGAGCTCGGGATGTACGAGCGCGCGTTCTCCGCTGCCGGCGCCGCCTTCGTCTCAGCTATCATCGTCAACCCTCTAGATGTCGCCAAGgtcggttcttcggggcactccctcgctcacgcagacctctcttccccgagtgttgtgtgcctccgctttggcgtctaatgcatttcctgtgtcttgatgcag

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G106703_T02 (Zea mays), 5'ss of exon 1
GGCCGCCGACCAGGAGCTCGGGATGGCCGAGCGCGCGCTCTCCGCCGCCGGCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcgggggg---ctttcgcttccgccg---cgtgcacttgtgtgattggtggctgaaagtttttttgtgttttttttttcgtttgctgcag--------
||  || |||||| |||| ||| ||  |||||||||||||||||||||||||||||| |||||||| || |||||||||||||||||||| || |||||||||||   | ||||    | ||| ||   || |     | | |    | || ||| |  | |    ||   |  |   | |  | ||||| |||           
GGGGGCGGACCAGCAGCTTGGGTTGTTCGAGCGCGCGCTCTCCGCCGCCGGCGCCGCCTTCGTCTCAGCTATCATCGTCAACCCTCTCGATGTTGCCAAGgtcggttcccggggcactccttcactcatgcaggcctctcctcccacgggagtggagtgttatgcgttcgcttcggcgtctaatgcgtttcctgtgtcgatgcag

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA04G41730.1 (Glycine max), 5'ss of exon 1
GGCCGCCGACCAGGAGCTCGGGATGGCCGAGCGCGCGCTCTCCGCCGCCGGCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgt-------------cggggtcggggggctttcgcttccgc-cgcgtgcacttgtgtga-ttggtggctgaaagtttttttgt-gttttttttttcgtttgctgcag
   |       |  |  | || || |  || || ||  ||||||||||||||||||| ||| ||||||||||||| ||||| || |||||||| ||||||||                 ||   || || ||   |    |    ||   || || |   || || | ||||  ||      | ||| ||||   ||| |       
ATTCAATTCTGATCAATTGGGAATCGGAGAACGAGCTTTCTCCGCCGCCGGCGCCGCCTTCCTCTCCGCCATCATTGTCAATCCCCTCGACGTTGCCAAGgtactctctcaattttattgttaaggagcgttaattctgacatatgtttcctagtctctcttcgttgttgaagattaaagaattgttgttttgagcgtct-------

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA06G13050.1 (Glycine max), 5'ss of exon 1
GGCCGCCGACCAGGAGCTCGGGATGGCCGAGCGCGCGCTCTCCGCCGCCGGCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcggggggctttcgcttccgccgcgtgcacttgtgtgattggtggctgaaagtttttttgtgttttttttttcgtttgctgcag----------
  |        |  |  | || || |  |  || ||  ||||||||||||||||||| ||| ||||||||||||| ||||| || |||||||| ||||||||   |          |||   ||  |  || || | || ||  || |||  |  |   | | ||| | ||  || ||  |  |  || |           
ATCTAATTCTGATCAATTGGGAATCGGAGCACGAGCTTTCTCCGCCGCCGGCGCCGCCTTCCTCTCCGCCATCATTGTCAATCCCCTCGACGTTGCCAAGgtaccgtctcaatttttttttgttatggagc-tgaaattctgatataggtttcctattctctctttttattcgttgttgagcgtcttgaatgcgttttaga

upper sequence: LOC_Os08g29720.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv16s0050g02360.t01 (Vitis vinifera), 5'ss of exon 2
GGCCGCCGACCAGGAGCTCGGGATGGCCGAGCGCGCGCTCTCCGCCGCCGGCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcggggggc-tttcgcttccgccgcgtgcacttgtgtgattggtggctgaaagtttttttgt---gttttttttttcgtttgctgcag-----
     ||||  | ||  |  || |    || ||  |  |||| ||||| ||||||||  || |||| |||||| |||| ||||||||||| |||||||||||  | ||     |   ||| | || |      |  |   |   || |    |  |||  | || || |   ||  | || ||  |||      |     
CAAATCCGAAAACGATATGCGGTTCTTAGAACGGTCATTCTCTGCCGCGGGCGCCGCTGTCCTCTCGGCCATCCTCGTTAACCCTCTCGATGTCGCCAAGgtatgtgttttatgttgttttggtttctaaattttgaaaagctcgactcaacgaagaatttcttgttattcagtcctcttattgatttttctttgatttt

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|218497482|gb|FG960434.1|FG960434
EST:     GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAG                         ACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
genomic: GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcg ... tttgctgcagACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
EST: gi|58667354|gb|CK056040.1|CK056040
EST:     GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAG                         ACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
genomic: GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcg ... tttgctgcagACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
EST: gi|7273806|gb|AU083350.1|AU083350
EST:     GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAG                         ACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
genomic: GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcg ... tttgctgcagACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
EST: gi|58693531|gb|CK082218.1|CK082218
EST:     ACCCTCTCGACGTCGCCAAG                         ACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
genomic: ACCCTCTCGACGTCGCCAAGgtcggggtcg ... tttgctgcagACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
EST: gi|58672713|gb|CK061399.1|CK061399
EST:     GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAG                         ACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
genomic: GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcg ... tttgctgcagACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
EST: gi|58607537|gb|CK035570.1|CK035570
EST:     GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAG                         ACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
genomic: GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcg ... tttgctgcagACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
EST: gi|7274031|gb|AU083575.1|AU083575
EST:     G-GCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAG                         ACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
genomic: GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcg ... tttgctgcagACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
EST: gi|29680567|gb|CB676842.1|CB676842
EST:     GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAG                         ACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
genomic: GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcg ... tttgctgcagACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
EST: gi|29677504|gb|CB673779.1|CB673779
EST:     GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAG                         ACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG
genomic: GCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcg ... tttgctgcagACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAG

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), 70 (downstream exon)
Score: 8

GGCCGCCGACCAGGAGCTCGGGATGGCCGAGCGCGCGCTCTCCGCCGCCGGCGCCGCGTTCGTCTCCGCCATCATCGTCAACCCTCTCGACGTCGCCAAGgtcggggtcg ... tttgctgcagACGAGATTGCAGGCGCAGGCGGCGGGGGTGCCCTACTACCAGCCGTCGCAGATGGCGTCGCTCGGCCCGGACGCG




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