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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g43150.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43150.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G004040_T01 (Zea mays), 5'ss of exon 10
AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaac-----cttatcacat-atttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcag-------
||||||||||||||| |||||||| |||||||||||||| ||||||||||| |||||||||||||||||||| ||||||||||| |||||||||||||||| ||        |||||  | ||  || || |||    ||  || ||||||| | | |  || || | |||||| ||  |        
AATAGATGCTGTGGGATCAACTAGGAAACAGTGGGAAGGGCACACAAAGAAGACATTGCATCAACTTCTTGTTGAGATGGATGGGTTTGAACAAAATGAGgcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatcttttatctcacag

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G156069_T01 (Zea mays), 5'ss of exon 10
AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaacct----tatcacat-atttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcag-------
||||||||||||||||||||||||||||||||||||||| ||||||||||| || ||||||||||||||||| |||||||| || ||||||||||||||||||  ||    |||||||| ||  || ||  ||  | |   || ||||||  | | |  || || | |||||| ||  |        
AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGGCACACAAAGAAGACGTTGCATCAACTTCTTGTTGAGATGGACGGGTTTGAACAAAATGAGgtatgctagtctatcacattatcaaatagagcaatatattcagaactttacctgactcttgcttccaattgatcttttatcttacag

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA06G13140.1 (Glycine max), 5'ss of exon 10
AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgta-acctta----tcacatatttaacagtccatcacacagaggactttatgt---aaattgtgttttctattgattttgcag
|||||||||||| ||||||||||| ||||| |||||||| || |||||||| |||||||| ||||| ||||| || |||||||| ||||| || ||||| ||| |  | |    | | | ||||   |||   | |         || | | |   || || |      | || || ||| ||
AATAGATGCTGTTGGTTCAACTAGGAAACAATGGGAAGGTCATACAAAGAAGACATTGCACCAACTACTTGTTGAAATGGATGGATTTGAGCAGAATGAAgtatatttcaagttttaaacatttgtgagtgtttaattagtttctctctgtttcctaatttattcaacatctttatcttgtag

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA13G08160.1 (Glycine max), 5'ss of exon 10
AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcag
||| |||||||| || ||||| |||||||| ||||| || ||||||||||| ||||||||||| || ||||| || |||||||| ||||| || ||||||||| | ||   |||  ||  |  |    |    |    |  ||||   ||||||  |  |   || || ||  ||
AATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTGAAATGGATGGGTTTGAGCAGAATGAGgtatctttga-acagcttggagtgcaatttgttcctctggtttta--gaaattgattcattattttatcttctag

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA14G29810.1 (Glycine max), 5'ss of exon 2
AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcag
||| |||||||| || ||||| |||||||| ||||| || ||||||||||| ||||||||||| || ||||| || |||||||| ||||| || ||||||||| | ||   |||  ||  |  |    ||   |    |  ||||   ||||||  |  |   || || ||| ||
AATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTGAAATGGATGGGTTTGAGCAGAATGAGgtatctttga-acagtttggagtgcaattcgttcctctggtttta--gaaattgattcattattttatcttgtag

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 10
AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaacctt---------atcacatatttaacagtccatcacacag------aggactttatgtaaattgtgttttctatt--gattttgcag
||| |||||||| || || || |||||||| |||||||| || |||||||| |||||||||||||| ||||| || |||||||||||||| || |||||||||    |          |    ||| |     |   |  | |        |||| | ||     | | || ||||||||  | || |||||
AATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTGAAATGGATGGTTTTGAGCAGAATGAGgtacttgttgattaggagtagtgtatcttgtgattacttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcag

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 5'ss of exon 10
AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttatcacatattt-----aacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcag
|||||||||||| || || ||  |||| || |||||||| || ||||| ||||||||||| ||||| ||||| || ||||||||||||||||| ||||||||||| |    ||| | ||     |  |||  ||        | | ||| | ||| |||  |    ||||  | ||| ||
AATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTGAAATGGATGGTTTTGAACAGAATGAGgtaacatatggacaaacttgtgttattagtgaatatttttctgcatttt-tttaacttggataa--tatttttcttgtag

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ36654 (Selaginella moellendorffii), 5'ss of exon 10
AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcag
 || || || || ||    | | | ||| | |||||||| ||||| ||||||||| || | ||||||||||| |||||||| || || |||  ||| |||||  |   ||    |   | |  |||| |  |            ||| |  |  |   |||  |||||| |||||
GATTGACGCCGTTGGAAGCAGTCGTAAAAACTGGGAAGGCCACACCAAGAAAACACTGAACCAACTTCTTGTGGAGATGGACGGATTCGAAGCAAACGAGgt--ctgcatgtgttgcctgat-gtcctttgc-----------catgcatttacttgcttcatttgattgtgcag

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|88369682|gb|CI582877.1|CI582877
EST:     GGTTTTGAACAAAATGAG                         GGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
genomic: GGTTTTGAACAAAATGAGgtaaccttat ... gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
EST: gi|51946127|gb|CV152468.1|CV152468
EST:     CTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAG                         GGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
genomic: CTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttat ... gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
EST: gi|29682022|gb|CB678297.1|CB678297
EST:     AAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAG                         GGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
genomic: AAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttat ... gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA

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: 62 (upstream exon), 51 (downstream exon)
Score: 33

AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttat ... gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA