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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcctctcttgcttgctccatctaatggctggataatgctgcag

Basic information

species Oryza sativa
transcript LOC_Os03g04970.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 15
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattt--tgttttcaattgttcctctcttgcttgctccatctaatggctggataatgctgcag--------------------------------------------------------------------------------------------------------------------------
||| ||||| ||||| |||||||| |  ||  |||||||  | || ||||| |||||||| |||||||| |||||||||||||| ||||||||||||||||||      |  | |||  || |||  ||| |   |||     | ||    | |  |||  ||  | | || ||                                                                                                                           
TGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTTGAAGgttagtgtttttcttttgctgattttcattttagatcttcca-tagcattgtttc-tggtagggcactactccacagatagtttctgtctcctcccttattcacttcaggcctcattctgcaatattttgagctttacttgcctctaagatgtatggtttaaccaacccttactacctgttctgacaaaaaatgcag

upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA10G25630.1 (Glycine max), 5'ss of exon 15
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcctctcttgcttgctccatctaatggctggataatgctgcag------------------------------
||| ||||| ||||| ||||| ||||||||  |||||||| | || ||||| |||||||| || ||||||||||||||||| || ||||||||||| ||||||        |    || |||   ||  ||||||| | |||  ||| |  |      | ||| |   | | |                              
TGGTGTTGCTCTTCTATATGCGTCAAAAGAGTTGGATAAACTTCAAACTGCTAACTTTGATCAGAAGATTGGTGTCCAGATTATCCAAAATGCTTTAAAGgttagttttctctgaattttttctgat--ttcctctttagctc-ctctaaatcgcattttgattacattacggatcttgtggaaggaaaaccagcaccagatt

upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA10G33680.1 (Glycine max), 5'ss of exon 15
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccatttt---gttttcaattgttcctctcttgcttgctccatctaatggctggataatgctgcag-------------------------
||| ||||| ||||| ||||||||||  ||  |||||||  | || ||||| |||||||| |||||||| || ||||||||||| ||||||||||||||||||      |  | |||     |||||| ||     | ||        |   |||  | | |   || | |  |||                         
TGGTGTTGCTCTTCTCTATGCATCAAGTGAGTTGGATAAGCTTCAAACTGCTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAGgttagtgtttttcttttgctgattttcattttagattatccatagcattgtttctggtaggtcactact-ccacagatttttctctctctcatcccttatt

upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA20G19980.1 (Glycine max), 5'ss of exon 15
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcct----ctcttgcttgctccatcta--atggctggataatgc----tgcag-----------------
||| ||||| ||||| |||||||| | |||  |||||||| | || ||||| ||||| |  |||||||||||||||||||| || ||||||||||| |||||         |    || |||   |||    ||    ||| | | |  | ||| |   |||  |  |   ||     ||  |                 
TGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTTAAAGgtcagttttctctgaattttttctgatttcctctttagctcctccatattgcattttttatgcttacactttgtatcttgtggaaggaaaaccagcacca

upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 13
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcctctct--tgcttgctc-catctaatggctggataatgctgcag--------
 || || || ||||| || ||| ||| |||  |||| ||| | |  || || ||||||||||| ||||||||||||||||| ||||| || || |||||||||| | | ||   ||| |   | || |  ||   |||  |  ||| |  ||   ||| | |  |    | |   |        
AGGTGTGGCTCTTCTATACGCAGCAAGAGAGTTGGAAAAACTTCCAACAGCCAACTTTGACCAGAAGATTGGTGTCCAGATTATTCAGAACGCATTGAAGgttttctattc---tttagaactaaaatcctctgatctgataattgatgacaagaaattgttttaacgagttttggtttaccag

upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 5'ss of exon 14
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcctctcttgcttgct-ccatct-aatggctggataatgctgcag-----------------------------------------------------------------------------------------------------------------------------
||| || || ||| ||||||| ||   ||| ||||| ||| | || ||||||||||||||||| ||||| || || || ||||| ||||||||||||| ||| | ||  || ||   |      |   || || |  |  ||||    ||||| | |  ||   ||| |  | |                                                                                                                              
TGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtat-catttctcaacctacccgtagaagt-ccacaatgacttgtggtcatctcagttactctttaacgaagtaattcatcacgatgcgtgttgagctagtaaaagattactctacggatgagggctaaagcatggttcaagattatctgttatgctaaagctttaaactcttctgagatgtaataaacttgtgttatag

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|88224758|gb|CI224607.1|CI224607
EST:     CCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAG                         ACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
genomic: CCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaat ... aatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
EST: gi|86493378|gb|CI136011.1|CI136011
EST:     CGAACTTTGACCNAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAG                         ACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
genomic: CGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaat ... aatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
EST: gi|88903313|gb|CI088851.1|CI088851
EST:     CCAGATCATTCAAAATGCTTTGAAG                         ACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
genomic: CCAGATCATTCAAAATGCTTTGAAGgtttacaaat ... aatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
EST: gi|86536911|gb|CI177117.1|CI177117
EST:     AAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAG                         ACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
genomic: AAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaat ... aatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
EST: gi|88842319|gb|CI081575.1|CI081575
EST:     AGATTGGTGTCCAGATCATTCAAAATGCTTTGAAG                         ACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT
genomic: AGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaat ... aatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATT

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: 55 (upstream exon), 74 (downstream exon)
Score: 9

TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaat ... aatgctgcagACCCCAGTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATTATTGGCAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcctctcttgcttgctccatctaatggctggataatgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG