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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCATGACTACAGGGGTGATGTGCTAGCACAGCTTAGCCCAGTCTTGCGAAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaaaaatgcagtatttggttactacttggatatgatgatagagttctgaactgtaacgtgcaaaacaacgctaactttgtatgatctgtcatcaacctttttttttcag

Basic information

species Oryza sativa
transcript LOC_Os03g13540.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13540.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G152477_T01 (Zea mays), 5'ss of exon 3
AATCATGACTACAGGGGTGATGTGCTAGCACAGCTTAGCCCAGTCTTGCGAAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaaaaatgcagtatttggttactacttggatatgatgatagagttctgaactgtaacgtgcaaaacaacgctaactttgtatgatctgtcatcaacctttttttttcag
|| ||||||||||||||||| | ||| || ||||| ||||| ||| |||| |||||||||   || ||||||||||| |  || ||| | || || ||||||   || |        |    || ||  | ||| ||| ||  |||  ||      | |    | ||| ||  | |  ||||   |||| |  | ||||   | |  || |   ||
AACCATGACTACAGGGGTGACGCGCTCGCGCAGCTGAGCCCGGTCCTGCGGAAGATCGACAGCCGGTTCATTTGCATCAAATCATTCGTCGTCAACGCAGgttcaaaga------tcgcgcgtgtttttttcttcgatctg--gattaaggaacagatta-ggcatgcgaa--agctgtaac---gtattacatatcattgccatccttctactag
















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|27576382|gb|CA999076.1|CA999076
EST:     AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAG                         AGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
genomic: AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaa ... tttttttcagAGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
EST: gi|58656595|gb|CK045275.1|CK045275
EST:     AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAG                         AGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
genomic: AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaa ... tttttttcagAGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
EST: gi|58593522|gb|CF991830.1|CF991830
EST:     AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAG                         AGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATA
genomic: AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaa ... tttttttcagAGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATA
EST: gi|58587652|gb|CF985960.1|CF985960
EST:     AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAG                         AGATTGTGGATTTCTTCTTTATCGACA
genomic: AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaa ... tttttttcagAGATTGTGGATTTCTTCTTTATCGACA
EST: gi|27576775|gb|CA999469.1|CA999469
EST:     AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAG                         AGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
genomic: AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaa ... tttttttcagAGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
EST: gi|58685580|gb|CK074267.1|CK074267
EST:     AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAG                         AGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
genomic: AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaa ... tttttttcagAGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
EST: gi|8527438|gb|AU092253.1|AU092253
EST:     TCGTTCATTGTTAATCCAG                         AGATTGTGNATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
genomic: TCGTTCATTGTTAATGCAGgtaggaaaaa ... tttttttcagAGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
EST: gi|117234872|gb|CT847928.1|CT847928
EST:     AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAG                         AGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
genomic: AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaa ... tttttttcagAGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
EST: gi|58659633|gb|CK048313.1|CK048313
EST:     AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAG                         AGATTGTGGATTTCTTCTTTATCG
genomic: AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaa ... tttttttcagAGATTGTGGATTTCTTCTTTATCG
EST: gi|27577370|gb|CB000065.1|CB000065
EST:     AAAGATCGACCAGCGATTCATTCGTATGAGGTCGTTCATTGTTAATGCAG                         AGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
genomic: AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaa ... tttttttcagAGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
EST: gi|58608007|gb|CK036040.1|CK036040
EST:     AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAG                         AGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT
genomic: AAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaa ... tttttttcagAGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATT

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), 73 (downstream exon)
Score: 104

AATCATGACTACAGGGGTGATGTGCTAGCACAGCTTAGCCCAGTCTTGCGAAAGATCGACCAGCGATTCATTTGCATGAGGTCGTTCATTGTTAATGCAGgtaggaaaaa ... tttttttcagAGATTGTGGATTTCTTCTTTATCGACACAACTCCATTTCAGCTGAAATATTGGACTCGCCCTAAAGACCATCATTATGACTGGAGAGGAGTGGCACCTCG




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