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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttacttcatttgcttttcttctttgctggtattattagaaaatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG

Basic information

species Oryza sativa
transcript LOC_Os05g26914.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g26914.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G856084_T01 (Zea mays), 3'ss of exon 3
gtgagttacttcatttgcttttcttctttgctggtattatt-----agaaaatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
||||| || ||| ||||  ||||| |||||||    |||||     | || |||     | ||||  || |||| | || |||| | |||||||||||||     ||||||||| |||||||||||||||||||||||||||||||| |
gtgagcta-ttcttttgtctttctgctttgcttaatttattgcttcaaaatatcttccattctgatttg-attttaaatcttaaatgacagGATTTCTATAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCG

upper sequence: LOC_Os05g26914.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G091811_T01 (Zea mays), 3'ss of exon 3
gtgagttacttcatttgcttttcttctttgctggtattatt-----agaaaatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
||||| || ||| ||||  || ||  ||||||   ||||||     | ||  ||     | || || ||||||| | || | || | |||||||||||||  |  ||||||||| |||||||||||||||||||||||||||||||| |
gtgagcta-ttcttttgtcttcctgttttgcttacattattgcttcaaaatgtcttccgttcttacttggatttaa-atatcaaatgacagGATTTCTATAACGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCG

upper sequence: LOC_Os05g26914.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G31080.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------gtgagttacttcatttgcttttctt----ctttgctggtattattagaa------aatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
                                                                                   | | | |||||  || || ||    || |         ||  |||      |||  | ||| |||| ||    || || | | ||  | |||||||  |||||    ||||| ||||||||||||||||||||||||||||| ||||| |
gtaagtttaaaatgcactcttcagcagtgatgagttccttttgtttgcgtgtgttttaaatatatgattttactttgtgaaaggatgcctcattgcctcttatttcaactgtataaagcccatgtgaattattcaatatattttactga-atatcctttatttgtcaacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAGCG

upper sequence: LOC_Os05g26914.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G14290.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------gtgagttacttcatttgcttttctt----ctttgctggtattattagaaa-atccagtttcctgacatggat----ttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
                                                                                   | | | |||||  || || ||    || |         ||  |||  || || | |  |    || ||    || || | | ||  | |||||||  |||||    ||||| ||||||||||||||||||||||||||||| |||||||
gtaagtttaaaatgcactcttcagcagtgatgagttccttttgtgagcatgtgttttaaatatgtgattgtactttgtgaaaggatgcctcattgcctcttatttcaactgtataaagcccatgtgaattattcaatatattactctgaatatcctttatttgtcaacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAGTG

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|58680824|gb|CK069511.1|CK069511
EST:     CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCT                         GATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
genomic: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
EST: gi|58673557|gb|CK062243.1|CK062243
EST:     CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCT                         GATTTCTATTCCAC
genomic: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCAC
EST: gi|58608089|gb|CK036122.1|CK036122
EST:     CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCT                         GATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGGAATC
genomic: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
EST: gi|29685207|gb|CB681482.1|CB681482
EST:     CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCT                         GATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
genomic: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
EST: gi|58692323|gb|CK081010.1|CK081010
EST:     CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCT                         GATTTCTATTCCACACTTGGTGTTTCAAGA
genomic: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCACACTTGGTGTTTCAAGA
EST: gi|29620923|gb|CB625934.1|CB625934
EST:     CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCT                         GATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
genomic: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
EST: gi|29680449|gb|CB676724.1|CB676724
EST:     CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCT                         GATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
genomic: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
EST: gi|29681007|gb|CB677282.1|CB677282
EST:     CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCT                         GATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
genomic: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
EST: gi|58660788|gb|CK049468.1|CK049468
EST:     CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCT                         GATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
genomic: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
EST: gi|29680374|gb|CB676649.1|CB676649
EST:     CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCT                         GATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC
genomic: CGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATC

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: 49 (upstream exon), 43 (downstream exon)
Score: 39

TAGTTTACAATCACGGACATCTTCTCGACTATTTAACCATGCACCATCACCGAGATTTCGCCATCGAAGGAGTTCAAGGTTCATTGTCAGAGCTGATGCTgtgagttact ... taatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtattattagaaaatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
                              atggatttgatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttacttcatttgcttttcttctttgctggtattattagaaaatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA