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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctactctcaactgtctggactccaatttttcctgtgagcttctggtgtccttccattagatactatcgttctaaaccaggcatgtatcatcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC

Basic information

species Oryza sativa
transcript LOC_Os03g57940.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g57940.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 14
ttctactctcaactgtctggactccaatttttcctgtgagcttctggtgtccttcc--attagatactatcgttctaaaccaggcatgtatcat---cattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC
   || | |     || |    ||    |  |     || | ||   ||| ||||   |||    ||| |   | ||   || |  || ||| |   | ||| ||||||||| ||||| |||||||| |||||||| |||||||| ||||||| ||| ||||| ||||| |||||||||||||| |||||||| || || ||| |
---tattttagctcgtttaacttctg--tgatgaaaggaacatcaactgttcttcagaatttatgactttatatttatctcatgtttgaatcctttactttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCAAATGGATAAACAAGAAGTGGAAAGAAGGATTCCATGTTACCTCAATGAC

upper sequence: LOC_Os03g57940.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
ttctactctcaactgtctggactccaatttttcctgtgagcttctggtgtccttccat-tagatactatcgttctaaaccaggcatgtatcatcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC
 ||     |||  | ||  ||    || ||| ||  ||| ||| | |  || |      |  |  |  |  | || |  |       | | ||    | ||||||||| || || ||||| || ||||||||||| || || ||||| | ||||||||| || |||||||||||||||||||| ||||| ||||| ||| |
gtcggtagtcacgtctcatgat---aactttgccaatgaacttattgattcataaagcatgaaagccgttttacttattccacttcatgtaat-gcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC

upper sequence: LOC_Os03g57940.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 14
-----------------------------ttctactctcaactgtc--tggactccaatttttcctgtgagcttctggtgtccttccatta-gatactatcgttctaaaccaggcatgtatcatcatt--acagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC
                             || ||      ||   |  | ||||  |     |   ||    |  |  |  || |  |  | |      || ||   ||    |    | |  | | |    ||||||  | || || ||||| || ||||||||||| || || ||||||| ||||||||| ||||| || |||||||||| ||||||||| || || ||| |
gttggtgttaatggtagtaatctgcaaatttttatgtcacacaaacacttgactatagaaaatgtcgtactttcattataaccatataacatggagtcttctttactaattttgtgcttgttgtaaattggtagGAACGTCTTATACTCAGCAATCTTACAAAGTCAGCGACTCTTTTCCTTTCAAGTGGATAAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGAC

upper sequence: LOC_Os03g57940.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
ttctactctcaactg--tctggactccaatttt--tcctgtgagcttctggtgtccttccattagatactatcgttctaaaccaggcatgtatcatcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC
    | ||||| |    | ||  |    | |||  || ||| |  ||      |  ||  | | |   | ||   | || |    |  | | |  | ||   ||||||||| || || ||||||||||||||||| |||||||||||||| |  || |||||||| || ||||||||||||||||||||||| ||||||||| |
--tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgttttgagttggc-ccatgtgtttatatggtgt-tttctgtttatgttagGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC

upper sequence: LOC_Os03g57940.1 (Oryza sativa), 3'ss of exon 14
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 13
ttctactctcaactgtctggactccaatttttcctgtgagcttctggtgtccttccattag---atactatcgttctaaaccaggcat--gtatcatcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC
        |   |  | |  | |  | || ||  |   |  || | || |      ||| |     |   ||||| ||   ||        | |  |  | ||||||||  |||| |||||||||||||||||||| ||||| || ||||| |  |||||||| || || || |||  |||||| ||| | || |||||||||||
---cgtcatagtcctttttaattttagttattttt--taatttttagttttgagttattcgtatgaatcttcgttgtagctcatctcccgattttgtgttaacagGAACATCATATACACAGCAGTCATACAAAGTGAGTGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGC

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|88669952|gb|CI724068.1|CI724068
EST:     GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAG                         GAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
genomic: GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
EST: gi|88247437|gb|CI247286.1|CI247286
EST:     AATGGAAGCTCATTGGTTGTAATGTCCAAAG                         GAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
genomic: AATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
EST: gi|88676859|gb|CI730972.1|CI730972
EST:     GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAG                         GAACTCCATACACACAGCANGTCCATTACANNAAGTCAGTGAATCNCTTTC
genomic: GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCA-GTC-AT-ACA--AAGTCAGTGAATC-CTTTC
EST: gi|87024580|gb|CI259295.1|CI259295
EST:     GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAG                         GAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
genomic: GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
EST: gi|88674676|gb|CI728789.1|CI728789
EST:     GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAG                         GAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
genomic: GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
EST: gi|88954921|gb|CI720286.1|CI720286
EST:     GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAG                         GAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
genomic: GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
EST: gi|88675791|gb|CI729363.1|CI729363
EST:     GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAG                         GAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
genomic: GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
EST: gi|87021813|gb|CI277980.1|CI277980
EST:     GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAG                         GAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
genomic: GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
EST: gi|29616080|gb|CB621092.1|CB621092
EST:     GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAG                         GAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
genomic: GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
EST: gi|58685128|gb|CK073815.1|CK073815
EST:     GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAG                         GAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
genomic: GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
EST: gi|88666711|gb|CI718847.1|CI718847
EST:     GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAG                         GAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
genomic: GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
EST: gi|58672924|gb|CK061610.1|CK061610
EST:     GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAG                         GAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA
genomic: GGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACA

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: 71 (upstream exon), 74 (downstream exon)
Score: 27

GATTGGATTATGGAGCAGTGGGAGAAGAATTATTACATAACGGCAATAGCAGGAGCAACCAATGGAAGCTCATTGGTTGTAATGTCCAAAGgttggtaaaa ... atcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgtccttccattagatactatcgttctaaaccaggcatgtatcatcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC
                         ttctaaa  putative branch site (score: 27)
           attagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctactctcaactgtctggactccaatttttcctgtgagcttctggtgtccttccattagatactatcgttctaaaccaggcatgtatcatcattacagGAACTCCATACACACAGCAGTCATACAAAGTCAGTGAATCCTTTCCTTACAAGTGGATTAACAAAAAGTGGAAAGAAGGTTTCCATGTGACATCTATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - -tgtctgg
- - - - - - - - - - - - - - - - cctgtga
- - - - - - - - - - - - - - - - - - - -gcttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgta