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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctaatataaatcaactcataagcttcttgttgcttttctttttctttgtagacattaaaatgccagtgcatatgctattttatgtgacttgagcaattctgttgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATTCAGGAAAATCAGGCTGAATTTCTCCGTCTGGTGAATGAATCTCCTGATA

Basic information

species Oryza sativa
transcript LOC_Os06g15360.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g15360.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G035417_T01 (Zea mays), 3'ss of exon 9
gtgctaatataaatcaactcataagcttcttgttgcttttctttttctttgtagacattaaaatgccagtgcatatgctattttatgtgacttgagcaattctgttgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATTCAGGAAAATCAGGCTGAATTTCTCCGTCTGGTGAATGAATCTCCTGATA
              |   |  |  | |  |  ||  | || |||  | || || |  |||| | | || | ||   | | |  |   ||| |||    ||| ||||||||   ||||||||||||||||||| || || || || || |||||  |||||||||||||||||||||| ||||| ||||||||  |||||||||||||||||||  
-----------gtgcttttactgtgttattccttagtattttttgacattttatattttaata-gtcatttcactgggtttggtcaatga-ttgtatgatt-tgttgattggtagCCAATGCTTCAAGAGCTAGGTAAACAAAACCCACAAATTCTGCGGTTGATTCAGGAAAATCAAGCTGAGTTTCTCCGCTTGGTGAATGAATCTCCTGAGG
















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|88847927|gb|CI006113.1|CI006113
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|29643187|gb|CB648194.1|CB648194
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|29657665|gb|CB653940.1|CB653940
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|29669285|gb|CB665560.1|CB665560
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|29643233|gb|CB648240.1|CB648240
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|300215820|gb|HO088446.1|HO088446
EST:     TTCCAAGCGCTGCTTGGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTG-CATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|33654536|gb|CF277150.1|CF277150
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|29662304|gb|CB658579.1|CB658579
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|29660321|gb|CB656596.1|CB656596
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|87015278|gb|CI275468.1|CI275468
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|86494540|gb|CI137173.1|CI137173
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|29673855|gb|CB670130.1|CB670130
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|29670072|gb|CB666347.1|CB666347
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|88830186|gb|CI076442.1|CI076442
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|29630613|gb|CB635622.1|CB635622
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|2431315|gb|C73735.1|C73735
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|300215841|gb|HO088467.1|HO088467
EST:     TTCCAAGCGCTGCTTGGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTG-CATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|14980837|gb|BI305515.1|BI305515
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|23514955|gb|BU673867.1|BU673867
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|29655833|gb|CB652108.1|CB652108
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGC
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGC
EST: gi|8859709|gb|AU097027.1|AU097027
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|218488797|gb|FG951622.1|FG951622
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|29631165|gb|CB636174.1|CB636174
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|87036144|gb|CI189591.1|CI189591
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|32947880|gb|BP184452.1|BP184452
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
EST: gi|8527786|gb|AU092601.1|AU092601
EST:     TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAG                         CCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT
genomic: TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATT

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: 48 (upstream exon), 69 (downstream exon)
Score: 41

TTCCAAGCGCTGCTTGCATTGGTCCAGGCTAATCCCCAAATCTTGCAGgtgctaatat ... tgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATTCAGGAAAATCAGGCTGAATTTCTCCGTCTGGTGAATGAATCTCCTGATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgccagtgcatatgctattttatgtgacttgagcaattctgttgattcacagCCAATGCTTCAAGAGCTTGGGAAGCAGAATCCGCAAATCTTGCGGTTGATTCAGGAAAATCAGGCTGAATTTCTCCGTCTGGTGAATGAATCTCCTGATA
                                          tgttgat  putative branch site (score: 41)
                                       ttctgtt  CT-rich tract
            atatgctattttat  TA-rich tract