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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_Os11g28340.1
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|117216901|gb|CT861591.1|CT861591
EST:     CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGG                         TGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
genomic: CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGGgtaagatcta ... gatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGA
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|58599124|gb|CK009652.1|CK009652
EST:     CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGG                         TGCATACCGTGTGCTGTATATCCTTAACTG
genomic: CGCACGAGGAATATTGACAACCTGACTGGCCAATATGTCTTCTTTCTAGGgtaagatcta ... gatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTG
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|33684131|gb|CF312370.1|CF312370
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttctagtttctgatataatgctatctctcaacacattttggtgatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA
          ttctgat  putative branch site (score: 3)
             tgatataat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgttatgttggatcttcattttgttcagtttcttgtattttgccatttctagtttctgatataatgctatctctcaacacattttggtgatgatgcagTGCATACCGTGTGCTGTATATCCTTAACTGGATCTACCGATACTTCACTGAGCCCCATTTCGTTCATTGGATAA

- - -tatgttg
- - - - - - - - - - - - - - - tttcttg
- - - - - - - - - - - - - - - - - - - - - tgccatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgat