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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacctttggcatttcacatctagttgcatgcaaactagctaattatatactacgacttattacatatatgatcataaattaactggcatgcagAGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g37000.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G457287_T01 (Zea mays), 3'ss of exon 1
----gtacgtacctttggcatttcacatctagttgcatgcaa--actagctaattatatactacgacttattacatatatgatcat-aaattaactggcatgcagAGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAG-------------
    |||  |  || |  | ||| | || ||         ||  | ||||| ||| |  | | | | |||  ||  ||  ||||||  || ||| |   |  ||||||| ||||||||||| |||||| |||||| ||||||| || || ||||| ||||||||||||   |||||| ||||||| || |||             
gtatgtatatctctctctctttttatatataaacagggaaaacaattagctgattgtgca-tgcaaattaaaactgatgagatcatcgaactaatt---aaacagAGCCCAGATGGAGATACCATAGACTGTGTGGACATCTCGAAACAGCCTGCGTTCGACCATCCTTCCCTCAAGAACCATACCATTCAGATGATGCCCTCCT
















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|86901781|gb|CI310543.1|CI310543
EST:     TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAG                         AGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA
genomic: TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAGgtacgtacct ... tggcatgcagAGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA
EST: gi|58612594|gb|CK040306.1|CK040306
EST:     TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAG                         AGCCTAGATGGAGATATCATAGATNGTGTGCACATCTCCAATCAACCTGCA
genomic: TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAGgtacgtacct ... tggcatgcagAGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA
EST: gi|88352833|gb|CI678859.1|CI678859
EST:     TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAG                         AGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA
genomic: TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAGgtacgtacct ... tggcatgcagAGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA
EST: gi|58611754|gb|CK039466.1|CK039466
EST:     TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAG                         AGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA
genomic: TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAGgtacgtacct ... tggcatgcagAGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA
EST: gi|33654001|gb|CF276615.1|CF276615
EST:     TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAG                         AGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA
genomic: TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAGgtacgtacct ... tggcatgcagAGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA
EST: gi|88429320|gb|CI690221.1|CI690221
EST:     TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAG                         AGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCANAC-TGC
genomic: TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAGgtacgtacct ... tggcatgcagAGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCA-ACCTGC
EST: gi|88738709|gb|CI762217.1|CI762217
EST:     TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAG                         AGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA
genomic: TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAGgtacgtacct ... tggcatgcagAGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA
EST: gi|88425735|gb|CI689388.1|CI689388
EST:     TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAG                         AGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA
genomic: TGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAGgtacgtacct ... tggcatgcagAGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCA

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: 49 (upstream exon), 65 (downstream exon)
Score: 14

CTTCTCGCCATCGGAAGCTACTTCGTCTACTTCTTTGCGGCGGCGGCAGGTGCGGAGCCTCCTCAAGCGCCTCAACAAGCCTCCCCTCGCAACCTTTCAGgtacgtacct ... tggcatgcagAGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaattatatactacgacttattacatatatgatcataaattaactggcatgcagAGCCTAGATGGAGATATCATAGATTGTGTGCACATCTCCAATCAACCTGCATTCGACCATCCTCTTCTCAAGGACCATACAATCCAG
                                      aattaac  putative branch site (score: 14)
                acttattacatatatg  TA-rich tract