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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttttacttgagtcatgccgtgatatatttgtagttagaattttgattttaggttttgtgttttgcatggttctaactgggtttctttttttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTA

Basic information

species Oryza sativa
transcript LOC_Os02g32030.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G113250_T01 (Zea mays), 3'ss of exon 1
---------gtttttacttgagtcatgccgtgatatatttgtagttagaattttgattttaggttttgtgttttgcatggttctaactgggtttctttttttg---gtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTA
         ||||| | || |||  ||   | || | | |||   || | | |   |  ||   |      ||  |||   |   ||     | | ||    |   | | |   ||| ||||| |||| ||||| | || |   |||||||||||||||||||||||  |||||||||||    ||||||||||| ||||| |         
gatttcagagttttcagtttagtt-tgttctcatgtttctgtg--taaattctcactaatatactcacaccttcacattactaacacactcataccttcgcagCAGGAATAAATATTGGTATTGGTAGTGTGATCTTCATAAGGAGTCAAGATGGTGAAGTTCACAGCTGAAGAGCTCCGTGCCATCATGGACAAAAAGAACA---------

upper sequence: LOC_Os02g32030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G095851_T01 (Zea mays), 3'ss of exon 1
-----gtttttacttgagtcatgccgtgatatatttgtagttagaattttgattttaggttttgtgttttg--catggttctaactgggtttctttttttggta-cagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTA
      ||||| ||   |    |    ||  | |||    ||||  || |  | | | ||||| | |||    | |  |  ||   |    ||   |    | |  |   ||| ||||| |||| ||||| |  | |   |||||||||||||||||||||||  ||||||||||||   ||||||||||| ||||| ||||      
cattactttttgctaccgatcagtgtcgaagtttttcagtttag--ttattttctcatgttttctatttaaatcttactgatatgcgaacctccaatggcagCAATAAATATTGGTATTGGTAGTGTGATATCTATAAGAAGTCAAGATGGTGAAGTTCACAGCTGAAGAGCTCCGCGCTATCATGGACAAAAAGAACAACA------

upper sequence: LOC_Os02g32030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G040369_T01 (Zea mays), 3'ss of exon 1
-----gtttttacttgagtcatgccgtgatatatttgtagttagaattttgattttaggttttgtgttttg--catggttctaactgggtttcttttttt-ggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTA
      ||||| ||   |    |    ||  | |||    ||||  || |  | | | ||||| | |||    | |  |  ||   |    ||   |    || | |   ||| ||||| |||| ||||| |  | |   |||||||||||||||||||||||  ||||||||||||   ||||||||||| ||||| ||||      
cattactttttgctaccgatcagtgtcgaagtttttcagtttag--ttattttctcatgttttctatttaaatcttactgatatgcgaacctccaatggcagGAATAAATATTGGTATTGGTAGTGTGATATCTATAAGAAGTCAAGATGGTGAAGTTCACAGCTGAAGAGCTCCGCGCTATCATGGACAAAAAGAACAACA------

upper sequence: LOC_Os02g32030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ28367 (Selaginella moellendorffii), 3'ss of exon 1
gtttttacttgagtcatgccgtgatatatttgtagttagaattttgattttaggttttgtgttttgcatggttctaactgggtttctttttttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTA------------------------------
                                                                              || ||   |  | |       |||||| |||   |   |     | |  | |||  |      |||||| ||||| | ||||||||| ||||||||||||||||||||| | |||||||| |                              
-----------------------------------------------------------------------------gtgagtgattcctct-------ggaattcgtagcggattctgacatcgtgatgctctttcca--gGTGAAATTCACGGCAGAAGAGCTGCGCCGGATCATGGACAAGAAGCACAACATCCGGAACATGTCTGTGATTGCTCATGTCGATCACG

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|88444119|gb|CI594492.1|CI594492
EST:     GAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: GAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|58588787|gb|CF987095.1|CF987095
EST:     -CA-T-CT-CT-CT-CTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|88731919|gb|CI753326.1|CI753326
EST:     CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|58593699|gb|CF992007.1|CF992007
EST:     CACTCCTCGTGCGTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: CACTCCTCCT-CCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|58672167|gb|CK060853.1|CK060853
EST:     CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|88395529|gb|CI613051.1|CI613051
EST:     GGGAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: GGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|117217683|gb|CT845087.1|CT845087
EST:     GGATCGGGAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: GGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|58591626|gb|CF989934.1|CF989934
EST:     CACTCCTCCGTCGTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: CACTCCTCC-TCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|58608952|gb|CK036985.1|CK036985
EST:     CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|88693181|gb|CI736756.1|CI736756
EST:     CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|88411944|gb|CI566673.1|CI566673
EST:     GGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: GGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|4879124|gb|AU063423.1|AU063423
EST:     CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGA-NGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|27554053|gb|CA997953.1|CA997953
EST:     CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|58682939|gb|CK071626.1|CK071626
EST:     GGATCGGGAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: GGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|58674100|gb|CK062786.1|CK062786
EST:     GAGG-GGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: GAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
EST: gi|5667333|gb|AU077575.1|AU077575
EST:     CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAG                         GAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC
genomic: CCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTC

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: 72 (upstream exon), 75 (downstream exon)
Score: 184

CCCCGCAGCGCCGCCGCCGCCACACACTCCCCCACATCTCCCCTTCCCTTCCACTCCTCCTCCTCCTCGGATCGGGAGGCGGAGCGAGCAATCCCCCAAGgtgatttcct ... tttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttaggttttgtgttttgcatggttctaactgggtttctttttttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTA
                          ttctaac  putative branch site (score: 184)
                                     tttctttttttggt  putative PPT
                                     tttcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttacttgagtcatgccgtgatatatttgtagttagaattttgattttaggttttgtgttttgcatggttctaactgggtttctttttttggtacagGAATTTGTATTTGTAGCGTGATTTGCAAAGCTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - catgccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgg