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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcactactcctctttctttcttcttcctctactactagtagattcgatcgattgatttctccctattctgttgtgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGCCTTATCTTCCCCGCCGACGCCATCGCGCGGGCCAAGCACTACCTCGCCA

Basic information

species Oryza sativa
transcript LOC_Os07g01760.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 3
-----------------------gtcactactcctctttctttcttcttcctctactactagtagattcgatcgatt-gatttctccctattctgttgtgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGCCTTATCTTCCCCGCCGACGCCATCGCGCGGGCCAAGCACTACCTCGCCA
                        || |  |  |      ||  ||  ||  | ||  ||  |    |   |      ||   | |   || | |||    || |||||| ||||||||||||||||| || ||||| |||||||| ||||| |||||||| || |||||  |||| ||||||| ||||||||||| ||| |||||||
gtcagggtcgccatctcatccgcatcgcatcctcatggagttggttgctcgacgacgccttctcttctttcttacccagacggcacttcatcccgttcccgtgcgcagGTGGTGGCGCTGTGCCAGGCTCCGTTCCTCCTCGATGACCCCAATGTCGGCCTCATGTTCCCGCCCGATGCCATCGTGCGGGCCAAGCGCTATCTCGCCA

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDP08011 (Chlamydomonas reinhardtii), 3'ss of exon 2
---------------gtcactactcctctttctttcttcttcctctactactagtagattcgatcgattgatttctccctat-tctgttgtgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGCCTTATCTTCCCCGCCGACGCCATCGCGCGGGCCAAGCACTACCTCGCCA
                  || | |||| | |       || |   |     ||         |  ||   |   |    |    | | ||   ||  |||||  | || ||||||   || ||||||||||| ||| | ||||| || |     || ||||||||||||||||||||||| |||||| |   ||| ||| 
catccgtgccagctgcctaccattcctgtctgccctagctccactttgagataccgttcctcactgacaaaccccgggatgcacccgctggtatgcacagGTGCTAGCCCTGTGCGCCGCGCCCTTCCTGCTGGATCACCCCAAGGTGGAGGACATGTTCCCCGCCGACGCCATCGCGCGTGCCAAGAAGATCCTAGCCT
















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|29615657|gb|CB620669.1|CB620669
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|29614592|gb|CB619605.1|CB619605
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|29684690|gb|CB680965.1|CB680965
EST:     CGCGCTCGGCCAGAA-CCTTCTCAGCTTCCCCCGGCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: CGCGCTCGGCCAGAAGCC-GCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|58589507|gb|CF987815.1|CF987815
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|29616796|gb|CB621808.1|CB621808
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|29615352|gb|CB620364.1|CB620364
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|29615840|gb|CB620852.1|CB620852
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|87005459|gb|CI285681.1|CI285681
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|58693367|gb|CK082054.1|CK082054
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|29676307|gb|CB672582.1|CB672582
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GATGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTGGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|29616434|gb|CB621446.1|CB621446
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|29614424|gb|CB619437.1|CB619437
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|29636374|gb|CB641383.1|CB641383
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|58693563|gb|CK082250.1|CK082250
EST:     TGCAACCCACACGCGCTCGTGCCAGAAGCCTGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: -GCAACCCACACGCGCTCG-GCCAGAAGCC-GCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|58687854|gb|CK076541.1|CK076541
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGGCAGGCCCCCTTTCCTTGCTCGATGATCCCAACGTCG
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCC-TTCC-TGCTCGATGATCCCAACGTCG
EST: gi|58694270|gb|CK082957.1|CK082957
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|29614163|gb|CB619176.1|CB619176
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
EST: gi|58593995|gb|CF992303.1|CF992303
EST:     TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAG                         GTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC
genomic: TCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGC

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), 75 (downstream exon)
Score: 203

GCGCGCCTCCGAGCTCCAGAAGGAGGGCAAGAAGATCATCTTCACCAACGTCGGCAACCCACACGCGCTCGGCCAGAAGCCGCTCACCTTCCCCCGCCAGgtcactactc ... tgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGCCTTATCTTCCCCGCCGACGCCATCGCGCGGGCCAAGCACTACCTCGCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactactagtagattcgatcgattgatttctccctattctgttgtgttgtgcagGTTGTGGCGCTGTGCCAGGCCCCCTTCCTGCTCGATGATCCCAACGTCGGCCTTATCTTCCCCGCCGACGCCATCGCGCGGGCCAAGCACTACCTCGCCA
                     gattgat  putative branch site (score: 203)
                      attgattt  TA-rich tract