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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcactcttaattttgtatgcttttcttgtttccagttgtctagccatttccagattttgtactactcatgtgtagtttgatgaagttcatgaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAAACTTTCAGTGAGCTCCTTTTGCAG

Basic information

species Oryza sativa
transcript LOC_Os04g56670.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56670.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G053767_T01 (Zea mays), 3'ss of exon 3
---gcactcttaattttgtatgcttttcttgtttccagttgtctagccatttccagattttgtactactcatgtgtagtttgatgaagttcatgaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAAACTTTCAGTGAGCTCCTTTTGCAG
   |  | || | | | | |     ||  | |||  |   |   | ||| |      |    ||||  |  | ||| || ||||| || |  | |||||||||||| || |||||||||||| |||||||| ||||| ||||||  ||||| ||||||||||||||| |||| |||||
gtcgttccctgattgtggcaatggattgatttttttaaaag--aaaccactattcagtgagctacttatt-tttgtggtctgatggagctacttaaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG

upper sequence: LOC_Os04g56670.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G053767_T04 (Zea mays), 3'ss of exon 3
---gcactcttaattttgtatgcttttcttgtttccagttgtctagccatttccagattttgtactactcatgtgtagtttgatgaagttcatgaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAAACTTTCAGTGAGCTCCTTTTGCAG-------------------------
   |  | || | | | | |     ||  | |||  |   |   | ||| |      |    ||||  |  | ||| || ||||| || |  | |||||||||||| || |||||||||||| |||||||| ||||| ||||||  ||||| ||||||||||||||| |||| |||||                         
gtcgttccctgattgtggcaatggattgatttttttaaaag--aaaccactattcagtgagctacttatt-tttgtggtctgatggagctacttaaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGGTCTCTTCCTCCCTCTCCCTCTTCC
















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|88347737|gb|CI655090.1|CI655090
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACCATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAAC-ATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAA
EST: gi|55432100|gb|CV729069.1|CV729069
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
EST: gi|88296234|gb|CI667624.1|CI667624
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTNGCTCGATAAGCT                         GTACAACATGGGTGTAATTCCAACAAAAAAGAGC
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGC
EST: gi|88334857|gb|CI648632.1|CI648632
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
EST: gi|218503821|gb|FG944828.1|FG944828
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACATGGGTGTAATGCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
EST: gi|33660819|gb|CF291786.1|CF291786
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
EST: gi|88330642|gb|CI635271.1|CI635271
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACATGGGTGTAATTCCAACAAAA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAA
EST: gi|87032242|gb|CI262024.1|CI262024
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
EST: gi|88309506|gb|CI655874.1|CI655874
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
EST: gi|86855599|gb|CI268926.1|CI268926
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACATGGGTGTAATTCCAACTAAAAAGAGCCTGTTAACATGTGAAAA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
EST: gi|88221415|gb|CI221371.1|CI221371
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
EST: gi|33693679|gb|CF321918.1|CF321918
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
EST: gi|55413423|gb|CV725799.1|CV725799
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAA
EST: gi|88329508|gb|CI648570.1|CI648570
EST:     CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCT                         GTACAACATGGGTGTAATTCCAACA
genomic: CCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACA

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: 65 (upstream exon), 68 (downstream exon)
Score: 17

GCATATGCCTGATGGTGCAAAAGCTCGTCAACATTATAAAGCAAATGGACCCGAGAGACCCTTACAGAGCGGAGATGACAGACATGTTGCTCGATAAGCTgtaagtagcc ... gaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAAACTTTCAGTGAGCTCCTTTTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttccagattttgtactactcatgtgtagtttgatgaagttcatgaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAAACTTTCAGTGAGCTCCTTTTGCAG
                             gtttgat  putative branch site (score: 17)
                                           atgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcactcttaattttgtatgcttttcttgtttccagttgtctagccatttccagattttgtactactcatgtgtagtttgatgaagttcatgaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAAACTTTCAGTGAGCTCCTTTTGCAG

- - - - - - -tgtatgc
- - - - - - - - - - -tttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgaa