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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgttatgttggatcttcattttgttcagtttcttgtattttgccatttctagtttctgatataatgctatctctcaacacattttggtgatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA

Basic information

species Oryza sativa
transcript LOC_Os11g28340.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g28340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G031802_T01 (Zea mays), 3'ss of exon 1
---gatgttatgttggatctt--cattttgttcagtttcttgtattttgccatttctagtttctgatataatgctatctctcaa-cacatt---ttggtgatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA
    ||| || | |   ||||  | |||||  |||   ||  || ||||   | ||||||||   |||||  |||||  || || |  |||   ||||| | |||||||||| ||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| || || |||||||
tatcatgctaggatcagtcttatccttttggacagagcct--taatttg---tctctagttt---atata-cgctattactaaagctgattcacttggttacgatgcagTGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA

upper sequence: LOC_Os11g28340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G46570.2 (Glycine max), 3'ss of exon 3
gatgttatgttggatcttcattttgttc-agtttcttgtattttgccatttctagtttctgatataatgctatctctcaacacattttggtgat--gatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA--------------------------
  | ||||   |  | ||||  |  ||  |  || |||| | ||   | | |  ||   | ||| ||| |    |   || ||  ||   ||     ||||||||||||| | |  || || || || ||||||||||| || ||||| ||||||||||| || || ||||||||||                          
attcttataa-gcttgttcaactcatttgaagtttttgtttgtttgaagtcc--gtgaatcataaaattcatgtttataatactattgtctggctcaatgcagTGCATACAGAGGACTATACATTCTCAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAGTATGATTCTCTCTTATTGTGTTTTA

upper sequence: LOC_Os11g28340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G46570.1 (Glycine max), 3'ss of exon 3
gatgttatgttggatcttcattttgttc-agtttcttgtattttgccatttctagtttctgatataatgctatctctcaacacattttggtgat--gatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA
  | ||||   |  | ||||  |  ||  |  || |||| | ||   | | |  ||   | ||| ||| |    |   || ||  ||   ||     ||||||||||||| | |  || || || || ||||||||||| || ||||| ||||||||||| || || ||||||||||
attcttataa-gcttgttcaactcatttgaagtttttgtttgtttgaagtcc--gtgaatcataaaattcatgtttataatactattgtctggctcaatgcagTGCATACAGAGGACTATACATTCTCAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA

upper sequence: LOC_Os11g28340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G25040.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------------------gatgttatgttggatcttcattttgttcagtttcttgtattttgccatttctagtttctgatataatgctatctctcaacacattttggtgatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA
                                                                |||      |||  | ||| | |||  ||   |||   |||| |         |  | | |||    | |  || |    | | |    |  |  ||||| |  |||||||   | || ||||| |||||||||||||| |||||||||||||| || || ||||| |||||||
gtacgatcttctttccataacttccctttacttgaaatttatcgttgcgtcgttctcttgactggatacatcattgactgttc-tcttgc-caaactctataatttagtttccctctgagtttcatacttcgattgctataccaataatgctctcttcttgcagGGGGTACCGTGGATTATACATCCTCAACTGGATCTACCGTTACTTCACTGAGCCGCACTTTGTTCACTGGATAA

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|88849104|gb|CI087626.1|CI087626
EST:     CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGG                         TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
genomic: CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGGgtaagatcta ... gatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
EST: gi|86542052|gb|CI182258.1|CI182258
EST:     CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGG                         TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
genomic: CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGGgtaagatcta ... gatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
EST: gi|86529172|gb|CI169378.1|CI169378
EST:     CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGG                         TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
genomic: CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGGgtaagatcta ... gatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
EST: gi|86886118|gb|CI321154.1|CI321154
EST:     CTTCTTTCTAGG                         TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
genomic: CTTCTTTCTAGGgtaagatcta ... gatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
EST: gi|27546640|gb|CA764760.2|CA764760
EST:     CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGG                         TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
genomic: CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGGgtaagatcta ... gatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
EST: gi|88262756|gb|CI366530.1|CI366530
EST:     AATATGTCTTCTTTCTAGGG                         TGCATACCGTGTGCGGTATATCCTTAACTGGATCTACCGATACTTCACTG
genomic: AATATGTCTTCTTTCTA-GGgtaagatcta ... gatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTG
EST: gi|88241404|gb|CI241253.1|CI241253
EST:     CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGG                         TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
genomic: CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGGgtaagatcta ... gatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
EST: gi|86545642|gb|CI185848.1|CI185848
EST:     CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGG                         TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
genomic: CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGGgtaagatcta ... gatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
EST: gi|89187774|gb|CI009758.1|CI009758
EST:     CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGG                         TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
genomic: CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGGgtaagatcta ... gatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA

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), 74 (downstream exon)
Score: 27

CCATATATTTAGAAGCTGTAGCAATTCTACCTCAACTTGTGTTGCTACAGCGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGGgtaagatcta ... gatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttctagtttctgatataatgctatctctcaacacattttggtgatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA
          ttctgat  putative branch site (score: 27)
             tgatataat  TA-rich tract