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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaaaacaccatatagacactaatagtagtttgtggctgtcacagcatttacttattataacactgataattgctttgtggattatcttcacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g53600.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53600.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G158562_T03 (Zea mays), 3'ss of exon 8
--------------------------------------------------------------------------------------------------tagaaaacaccatatagacacta-atagtagtttgt--ggctgtcacagcatttacttattataacactgataattgctttgtggattatcttcacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG
                                                                                                    ||||   |   | |   | || ||| | || |||  |||||   || || ||  || || | ||| |  |    | | |       |||||||| ||| ||||||||||||| ||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
gtaagataacctcttcctcccttagtttatttaatttacttctataattatgatgtgtttatgtgtattagatcattaagttattttttagctccttggtgaaagtgcatgacaagtagtagatacttgtgtgtttggctgatgcaacaattgttt-ttgttacaatatttggcgttgttgctggcatcttcaccatttagGGCTGGGTGGCTTTTCGTCAAGGAGTGGAATGCGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG

upper sequence: LOC_Os01g53600.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA06G19740.1 (Glycine max), 3'ss of exon 10
tagaaaacaccatatagacactaatagtagtttgtggct-gtcacagcatttacttattataacactgataattgctttg-----tggattatcttcacaatta----agGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG
     || |  ||     |  |  || | | ||   | |  | | | | ||||  | || | ||||| | | ||   |       |  |||||||     |||     |||  |||| || ||| || |||||   |||||||||||| || ||  |||| ||||||||||| ||||| ||||| ||||||||||||
---gtaagagaattgttccttttctactggcttacagttcataagaacttttaagt-ttctgacactta-agttatatgaacgatttaattatctgaggcattgcattagGAATGGGCGGTATTCCGGCAAGGTAAGGAATGTGGATTCCAGGGGAGAACAAATAAATTGGTGGATGGATGCTATTCCTTTTGGCAG

upper sequence: LOC_Os01g53600.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G23780.1 (Glycine max), 3'ss of exon 10
--tagaaaac-accatatagacactaat----agtagtttgtg---gctgtcacagcatttacttattataacactgataattgctttgtggattatcttcacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG
   ||| ||        |   ||||       |||  || |       | | |     || ||||    | | |   || |||   || |      | ||  || |  ||| |||||||| ||| || |||||   |||||||||||| || ||  |||| |||||| |||| ||||| ||||| ||||||||||||
gtaagagaattgttcctttcccactggcttccagttattcggatgaatttttaagttgttgacttgaagttatatgaatgatttaattatctgaggtgtt-gcatt--agGACTGGGTGGTATTCCGACAAGGTAAGGAATGTGGATTCCAGGGGAGAACAAATAAACTGGTGGATGGATGCTATTCCTTTTGGCAG

upper sequence: LOC_Os01g53600.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv14s0066g01310.t01 (Vitis vinifera), 3'ss of exon 10
tagaaaacaccatatagacacta--atagtagtttgtggctgtc-acagcatttac--ttattataacact-gataattgctttgtggattat-cttcacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG
        |  || ||||  |||  ||  | |||  |     || || |   | |   | || |  |  || | ||||| |||| ||  |||  | |     |  |||  ||||||| |||||| ||||| || ||  |||| || || ||  |||| ||||||||||||||||||||||| ||||||||||||
-------tattatctagatgctataatttttgttgatacaaatctactgtgatgatgatcatgaccatgcttggtaatttctttttgatttaaacattgttttgcagGATTGGGTGGTATTTCGACAAGGTGTTGAGGGTGGTTTCCAGGGCAGAACCAATAAATTGGTTGATGGTTGCTATTCCTTTTGGCAG

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|29674660|gb|CB670935.1|CB670935
EST:     CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATT                         GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
genomic: CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATTgtaaggaaac ... cacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
EST: gi|218480035|gb|FG968183.1|FG968183
EST:     CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATT                         GGTTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
genomic: CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATTgtaaggaaac ... cacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
EST: gi|29645257|gb|CB650264.1|CB650264
EST:     ACAAACTTGATTTGGCTAGCTTGATT                         GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
genomic: ACAAACTTGATTTGGCTAGCTTGATTgtaaggaaac ... cacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
EST: gi|29674619|gb|CB670894.1|CB670894
EST:     CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATT                         GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
genomic: CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATTgtaaggaaac ... cacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
EST: gi|29674661|gb|CB670936.1|CB670936
EST:     CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATT                         GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
genomic: CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATTgtaaggaaac ... cacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
EST: gi|29674620|gb|CB670895.1|CB670895
EST:     CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATT                         GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
genomic: CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATTgtaaggaaac ... cacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
EST: gi|29645420|gb|CB650427.1|CB650427
EST:     CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATT                         GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
genomic: CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATTgtaaggaaac ... cacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
EST: gi|29640149|gb|CB645158.1|CB645158
EST:     CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATT                         GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
genomic: CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATTgtaaggaaac ... cacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
EST: gi|29661886|gb|CB658161.1|CB658161
EST:     CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATT                         GGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT
genomic: CGATGATCCTGCTTAACGAAGTGGACAAACTTGATTTGGCTAGCTTGATTgtaaggaaac ... cacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatttacttattataacactgataattgctttgtggattatcttcacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG
                                      ttatcttc  CT-rich tract
     tacttattataaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaaaacaccatatagacactaatagtagtttgtggctgtcacagcatttacttattataacactgataattgctttgtggattatcttcacaattaagGGCTGGGTGGCATTTCGCCAAGGAGTGGAATGTGGATTTCAAGGACGAACTAATAAATTGGTTGATGGTTGCTACTCCTTTTGGCAG

- - -aacacca
- - - - - - - - -acactaa
- - - - - - - - - - - - - - - - -gtggctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctttg