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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgttttgtatgtatatctagaaacttttgaagaccgtcactagctgaaatttttttagatggaaatttgtgaattgattatcgcataactttacttgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCATATGCCGTGGACGGACATTCCATGCACCGAGTGAGATTTCATTTTAGGA

Basic information

species Oryza sativa
transcript LOC_Os08g10600.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10600.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G155729_T01 (Zea mays), 3'ss of exon 14
gtaacgttttgtatgtatatctagaaacttttgaagaccgtca-ctagctgaaatttttttagatggaaatttgtgaattgattatcgcataactttacttgtacttc-agGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCATATGCCGTGGACGGACATTCCATGCACCGAGTGAGATTTCATTTTAGGA
||||    ||| |    ||      |  ||||| |  | |||| | || | | | | |||| ||||| ||    |  |||| || |   | ||| || | |||||||| ||| |||||||||||||| ||| |||||||||| |||||||| || ||||| |||||| ||||| | |||||||||||||| |||||||||||||| |||| 
gtaa----ttgcagccctagtatatatgttttggaatctgtcagcaaggtaagaatatttttgatgggaacacattgattg-ttgt--taaaacattgcctgtacttccagGAGTTGAAGTTTCTCCGCTTTGCTCTTATGCTGGAGAGAATCTAGAAGCTATATGCAGTGGAAGAACATTCCATGCACCAAGTGAGATTTCATTCTAGGC

upper sequence: LOC_Os08g10600.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 14
-------------------------------------------------------------------------------------gtaacgttttgtatgtatatctagaaacttttgaagaccgtcactagctgaaatttttttagatggaaatttgtgaattgattatcgcataactttacttgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCATATGCCGTGGACGGACATTCCATGCACCGAGTGAGATTTCATTTTAGGA
                                                                                       ||  | |   ||  |||  | || |  |   |      |   |||   ||   |  |   ||  || | | |   ||  | ||   ||  |  | |   || ||||||||||||||| || |||||  | || ||||| || || ||||||||| | ||||| || ||| | ||||| ||||||||  ||||||| |||||||||  
gtaggttatttactctttatttccaaggagaagaaatatagttgcggccggactcttacccagacatatgtatacacacatggagagaatatgtgacataaatagatggagagatagtatattttttgttagaaaaatgatggtcttatctaactctttttcttt-tcatgaaatgtccctgccctta-ttcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCTATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCATTTTAGTT
















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|88244522|gb|CI243644.1|CI243644
EST:     CGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: CGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|88249120|gb|CI248969.1|CI248969
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACTTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|3762886|gb|AU029638.1|AU029638
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|58676490|gb|CK065177.1|CK065177
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|218484530|gb|FG955871.1|FG955871
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|8860129|gb|AU097447.1|AU097447
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|29685401|gb|CB681676.1|CB681676
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|86425777|gb|CI070874.1|CI070874
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|218481588|gb|FG958598.1|FG958598
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|88958308|gb|CI095827.1|CI095827
EST:     CAGGTGGCTTTTTGACTCATTCCGTGCCCTNGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: CAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|29674853|gb|CB671128.1|CB671128
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|29616665|gb|CB621677.1|CB621677
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|58653914|gb|CK042594.1|CK042594
EST:     GGTATCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|8858093|gb|AU095411.1|AU095411
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|58685945|gb|CK074632.1|CK074632
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|88974625|gb|CI022951.1|CI022951
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|3767528|gb|AU031622.1|AU031622
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|29685402|gb|CB681677.1|CB681677
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|58607867|gb|CK035900.1|CK035900
EST:     GGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|29289881|gb|CB483495.1|CB483495
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
EST: gi|88961208|gb|CI096612.1|CI096612
EST:     GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAG                         GTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA
genomic: GGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCA

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: 64 (upstream exon), 68 (downstream exon)
Score: 17

ACTCCTGATAGTGCCAGATTAATGCTGCTCCGCCTTCACAGCCGATGGGTGGTAGCTGCAGGTGGCTTTTTGACTCATTCCGTGCCCTTGTATATGACAGgtaacgtttt ... tgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCATATGCCGTGGACGGACATTCCATGCACCGAGTGAGATTTCATTTTAGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttagatggaaatttgtgaattgattatcgcataactttacttgtacttcagGTGTTGAAGTTTCTCCACTTAGCTCTTATGCGGGAGAGAACCTGGAAGCCATATGCCGTGGACGGACATTCCATGCACCGAGTGAGATTTCATTTTAGGA
                                gcataac  putative branch site (score: 17)
                                      ctttactt  CT-rich tract
                     aattgattat  TA-rich tract