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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaactgtgcagctgctgcaaacaatctattcattcgaatggaagacagaattaatgttttctctgaatcccgtgtgtttcagATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAGACGTACGTCATATTCGGGGAGGCCAAGATCGAGGACCTGAGCTCCCAGC

Basic information

species Oryza sativa
transcript LOC_Os03g02960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G171466_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------------------------------gtaagaaactgtgcagctgctgcaaacaatctattcattcgaa--tggaagacagaattaatgttttctctga--atcccgtgtgtttcagATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAGACGTACGTCATATTCGGGGAGGCCAAGATCGAGGACCTGAGCTCCCAGC
                                                                                                |||| | |    || |||  |   |||| | ||  || |    ||         |||| |||  |   ||    || |   |  |||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||||||||| ||||
gtacgtatatctatatatatatgccaattattgccacaaggaaggaacacgatagatagctaactttttatgctccgtgtatacaattttacaaacaagatagtagatagatgcc-cgtgcaattt-ttagttagctcttgccttctcatattactgtcatgcgtgtctgtctcccttccttcagATACTGTTCGTGGTGTCGAAGCCGGACGTCTTCAAGAGCCCGACGTCGGAGACGTACGTGATATTCGGCGAGGCCAAGATAGAGGACCTGAGCTCACAGC

upper sequence: LOC_Os03g02960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G49470.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagaaactgtgcagctgctgcaaacaatctattcattcgaatggaagacagaattaatgttttctctgaatcccgtgtgtttcagATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAGACGTACGTCATATTCGGGGAGGCCAAGATCGAGGACCTGAGCTCCCAGC
|||| |   |   | | |    |||  | | ||    ||    ||   |   || |  |    | | ||  ||    ||| | |||| | || ||| |  | || |||||||| ||||| |||||||||   || || || || || |||||||| |||||||||||||||||  ||||||| ||||
gtaa-acctttctctgttttctcaataagtttagatttttttctgcgtgtgtgattctaatgatacactacatta-atgt-tatcagGTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAAACCTATGTTATATTCGGTGAGGCCAAGATCGAGGATTTGAGCTCTCAGC

upper sequence: LOC_Os03g02960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 3
gtaagaaactgtgcagctgctgcaaacaatctattcattcgaatggaagacagaattaatgttttctctgaatcccgtgtgtttcagATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAGACGTACGTCATATTCGGGGAGGCCAAGATCGAGGACCTGAGCTCCCAGC
|||| |   |||     | |||       | |||||| | | ||     |     || |    || |     ||| | |  |  |||||| | ||  |  | || |||||||| ||||||||||| || |  || ||||| || |||||||| |||||||| ||||| |||||  ||||||| ||||
gtaaaattttgtctgatttctgt---tcttgtattcacttgtatcatgaatgttctttaccagtttt-----tcctgggcttggcagATATTATTTTTCATCTCAAAGCCTGATGTCTTCAAGAGTCCAAATTCAGAGACCTATGTCATATTTGGGGAGGCGAAGATAGAGGATTTGAGCTCTCAGC

upper sequence: LOC_Os03g02960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
gtaagaaactgtgcagctgctgcaaacaatctattcattcgaatggaagacagaattaatgttttctctgaatcccgtgtgtttcagATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAGACGTACGTCATATTCGGGGAGGCCAAGATCGAGGACCTGAGCTCCCAGC
                           || || | | || | |      | |||||  |   |  ||  |  ||  ||   || ||||||||||| ||| | |||||||| ||||| |||||||||||| | || || ||  || |||| || || |||||||||||||||||| |||| |||||||
-------------------------gtaagct-tgcgttggtagatcgaagagaatagagactaacttcgcttctggttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

upper sequence: LOC_Os03g02960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ21445 (Selaginella moellendorffii), 3'ss of exon 1
gtaagaaactgtgcagctgctgcaaacaatctattcattcgaatggaagacagaattaatgttttctctgaatcccgtgtgtttcagATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAGACGTACGTCATATTCGGGGAGGCCAAGATCGAGGACCTGAGCTCCCAGC
                           || ||          ||| |||  |||||  |   |  ||  |   |  ||   || ||||||||||||||| | |||||||| ||||| |||||||||||| | || || ||  || |||| || || |||||||||||||||||| |||| |||||||
-------------------------gtaagcttgcgtagtagatgaaag--agaatagagtctaacttcgctccttgttctttccagATACTGTTCGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

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|86899298|gb|CI298138.1|CI298138
EST:     TGAAACCCGTCACGGGAGTCAGCAGGATTACCATCAAGAGAGCCAAGAAT                         ATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAG
genomic: TGAAACCCGTCACGGGAGTCAGCAGGATTACCATCAAGAGAGCCAAGAATgtaagaaact ... tgtgtttcagATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAG
EST: gi|87012968|gb|CI297195.1|CI297195
EST:     AGCAGGATTACCATCAAGAGAGCCAAGAAT                         ATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAG
genomic: AGCAGGATTACCATCAAGAGAGCCAAGAATgtaagaaact ... tgtgtttcagATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAG
EST: gi|86417949|gb|CI032158.1|CI032158
EST:     AGCAGGATTACCATCAAGAGAGCCAAGAAT                         ATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAG
genomic: AGCAGGATTACCATCAAGAGAGCCAAGAATgtaagaaact ... tgtgtttcagATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAG

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), 71 (downstream exon)
Score: 40

GCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGGAGTCAGCAGGATTACCATCAAGAGAGCCAAGAATgtaagaaact ... tgtgtttcagATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAGACGTACGTCATATTCGGGGAGGCCAAGATCGAGGACCTGAGCTCCCAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcattcgaatggaagacagaattaatgttttctctgaatcccgtgtgtttcagATACTGTTCGTGGTGTCCAAGCCTGACGTCTTCAAGAGCCCGACGTCGGAGACGTACGTCATATTCGGGGAGGCCAAGATCGAGGACCTGAGCTCCCAGC
                     aattaat  putative branch site (score: 40)
                   agaattaatgtttt  TA-rich tract