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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgcatttgtattttctttactcagatattttgtccactttattaggttgcctgacgaaatgttttcttttag

Basic information

species Oryza sativa
transcript LOC_Os06g39640.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 17
lower sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 16
GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgcatttgtattttctttactcagatattttgt-ccactttattaggttgcctgacgaaatgttttcttttag
||| ||||| ||||||||||| ||||| ||||||||||| || ||||| ||||| ||||| |||||| | |||||||   |||| ||     |  | || |   || ||| ||   |||  || || |  || || |||| ||
GGACGGTGTTAGTGAAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAGgttgggtgcatttaattttttttcttctaattcttctaagccccttcatagagtttactaactag-tgcttactttcag

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G079080_T02 (Zea mays), 5'ss of exon 17
GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgcatttgtat-tttctttactcagatattttgtccactttattaggttgcctgacgaaatgttttcttttag
||| ||||| |||||||| || ||||| ||||||||||| || ||||| ||||| ||||| |||||| | |||||||  || ||| |||| ||     || |   | | ||||   |||  || || |   ||||| ||  ||
GGACGGTGTTAGTGAAGGTCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGGAAGgttgggtgcattttaatgtttttttattc-----ttctaagctccttat--agtttactaactag-cgtttttttccag

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA10G00530.1 (Glycine max), 5'ss of exon 9
GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgcatttgtattttctttactcagatatttt----gtccactttattaggt-tgcctgacgaaatgttttcttttag
||||||||| |||||||| ||||| ||||||||||| || |||||||||||||| || || ||||| |||     ||  | ||||||   ||| || || |    |  || ||||| |    ||||      ||| | |  ||  ||
GGATGGTGTAAGTGAAGGGCAATTTTACCAAGTTCTACTTTATGAGTTGGATGCAATTCGGAAGgtcagaattgatt--actttcttccatcaaatgttctaataggtcattttataacacgtgcccacaagaatatatatttgcag

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA20G28970.1 (Glycine max), 5'ss of exon 18
GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgcatttgtattttctttactcagatattttgtccactttattaggttgc-ctgacgaaatgttttcttttag
||| ||||| |||||||| ||||| ||||||||| | || |||||||||||||| || || ||||| ||   || ||    |   | ||| |   | || |    |  | |      ||  ||||  |  | | |   | |||
GGACGGTGTAAGTGAAGGGCAATTTTACCAAGTTTTACTTTATGAGTTGGATGCGATTCGGAAGgtcaggatcactttctctcattatacacttgttttcttattatgtcaaagatatgttctgagaagttatatctgtgtag

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA02G00510.1 (Glycine max), 5'ss of exon 17
GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgcatttgtattttctttactcagatatt--ttgtccactttat----taggttgcctgacgaa-atgttttcttttag
||||||||| |||||||| || || ||||||||||| || |||||||||||||| || || ||||| |||     ||   | |||    |  |  |  |  | |  || |||||     | |||  |  | ||| || |||  ||  ||
GGATGGTGTAAGTGAAGGGCAGTTTTACCAAGTTCTACTTTATGAGTTGGATGCAATTCGGAAGgtcagaattgattacttattcccatcataagttctagtaggtcattttataacacatgttctcacaagaatatatttatttgcag

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 17
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 5'ss of exon 17
GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgcatt-tgtattttctttact--------cagatattttgtccactttattaggttgcctgacgaaa---tgttttcttttag
 ||||| || || ||||| |||||||| |||||| | ||||||||||||||||| || || ||||| | |    || || ||    |  | |        || | | || |   |   | |||  |   | ||        ||| ||  |||||
TGATGGAGTAAGCGAAGGGCAATTCTATCAAGTTTTACTCTATGAGTTGGATGCAATTCGAAAGgtaaaaacttttgtgcatagcatgaaatgaatccgccacaaagttagcaaaacattttacataatcggaaacgggtttgtgtttgtttag

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 5'ss of exon 17
GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgc--atttgtatttt-ctttactcagatattttgtccactttattaggttgcctgacgaaatgttttcttttag
|||||||||||||||||| || |||||||| ||||| || |||||  | ||||| || || |||||| | | |  | |  ||   | | |||   ||| || ||      | |  ||   || |||     |             
GGATGGTGTCAGTGAAGGGCAGTTCTACCAGGTTCTACTATATGAACTTGATGCCATTCGTAAGgttggttaccaactgataccatgccttatcaagacatctttcatgttcttatatagtgtctgtgtctag------------

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 17
lower sequence: EFJ14096 (Selaginella moellendorffii), 5'ss of exon 16
------------------------------------GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgcatttgtattttctttactcagatattttgtccactttattaggttgcctgacgaaatgttttcttttag
                                     |||||||| || ||||| || |||||||||||||||||  | ||||||||||| ||  | ||||||   |        | ||     | | |   |||  |  |    | || |   |                       
CTCTGGATACAAACCTGGAAGAATCATCTTCTACAGAGATGGTGTGAGCGAAGGACAGTTCTACCAAGTTCTCCTTCACGAGTTGGATGCAATTAGAAAGgtttagtatggaaagacttggcgcattgactgattcagctcttcgttttggacag-----------------------

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|29636941|gb|CB641950.1|CB641950
EST:     ATGAGTTGGATGCTATCCGCAAG                         GCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTT
genomic: ATGAGTTGGATGCTATCCGCAAGgttagatgca ... tttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTT
EST: gi|29674861|gb|CB671136.1|CB671136
EST:     AAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG                         GCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTT
genomic: AAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgca ... tttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTT
EST: gi|29636972|gb|CB641981.1|CB641981
EST:     AAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG                         GCATGTGCATGTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTT
genomic: AAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgca ... tttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTT

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: 53 (upstream exon), 36 (downstream exon)
Score: 7

GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgca ... tttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTTGTCCAAAAGCGTCACCATACAAGACTCTTCGCAAACAATCACAAAGACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAGgttagatgcatttgtattttctttactcagatattttgtccactttattaggttgcctgacgaaatgttttcttttag

- - - - - - - - - - - - - - - - - CTCCTC