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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgtaattgtagctgtagcttagtgaaacgtttctctttgcaattgtaaaatctctccaaattcccataagatcactgattttgcatgcacacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACTGCCCTTGGAGCTGCGTATGCAGCTGGATTAGCTGTTGGAGTCTGGTCGA

Basic information

species Oryza sativa
transcript LOC_Os04g55410.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G023163_T01 (Zea mays), 3'ss of exon 3
-------ggtgtaattgtagctgtagcttagtgaaacgtttctctttgcaattgtaaaatctctccaaattcccataagatcactgattttgcatgcacacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACTGCCCTTGGAGCTGCGTATGCAGCTGGATTAGCTGTTGGAGTCTGGTCGA
        |||| ||  || |||   |  |    |    ||   |||     | |  |||  |     ||  |   | |||  ||   ||    | |   |||||||||||||||||| || ||||||||||||||||| |||||||| ||||| || ||||| |||||||| ||||| ||||| || ||||  ||||| ||| | |
cttaacttgtgtgatcttacctggcacagatcttattcatttatttt----ctttgcaattgcattggatgactg-aggatagcttggttac--ttcctgcctgcagGCTGATTTATTAGGCAGCCCTGTTGTCAGACCAGCTGACATAGAGACCACAGCCCTCGGAGCTGCATATGCTGCTGGGTTGGCTGCAGGAGTTTGGACCA

upper sequence: LOC_Os04g55410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G22870.1 (Glycine max), 3'ss of exon 3
ggtgtaattgtagctgtagcttagtgaaacgtttctctttgcaatt----gtaaaatctctccaaattcccataagatcactgattttgcatgcaca----cctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACTGCCCTTGGAGCTGCGTATGCAGCTGGATTAGCTGTTGGAGTCTGGTCGA
        |   | |     ||| ||||  |||  | ||   |  |    | |||| || |   | ||  || |  |    | | |||   |  | |     || ||||| |||||  ||||  | ||  |  | |||||||||||||| |||||||| || |||||||| || ||||| || ||||||||| ||||  | |||    
--------tactgttaatagttactgaagtgttcatgttcataggttgatgcaaaaccttttttacttttcacataactgataaatttttgttaataatgttctacagGCAGATTTGGTGGGATGTCCAATAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCAGGATTAGCTATTGGGATTTGGAAAG

upper sequence: LOC_Os04g55410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G03230.1 (Glycine max), 3'ss of exon 2
ggtgtaattgtagctgtagcttagtgaaacgtttctctttg-caattgtaaaatctctccaaattcccataagatcactgattttgcatgcaca----cctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACTGCCCTTGGAGCTGCGTATGCAGCTGGATTAGCTGTTGGAGTCTGGTCGA
    | ||  | | ||    | ||   |   |   | |  |     || |||| || |  |  ||  || |  |    | |||||   |    |     || ||||| |||||  ||||  | || ||  | |||||||||||||| |||||||| || |||||||| || ||||| || |||||||||  |||  | |||    
----tcatgtttgttgagaatcagaataggatcagtttcagattgatgcaaaagctttttac-ttttcacataactgataattttttgttactaatgttctacagGCAGATTTGGTGGGATGTCCAGTAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCCGGATTAGCTACTGGGATTTGGAAAG

upper sequence: LOC_Os04g55410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv09s0002g07860.t01 (Vitis vinifera), 3'ss of exon 3
ggtgtaattgtagctgtagctta-gtgaaacgtttctctttgcaattgtaaaatctctccaaat-tcccataagatcactgattttgcatgcacacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACTGCCCTTGGAGCTGCGTATGCAGCTGGATTAGCTGTTGGAGTCTGGTCGA
|   | ||  | |  ||| ||||  | | ||    |    | | ||  |    |   |  || | |   ||  ||  | |  |  ||  |    |  ||||||||||| | ||||| | ||| || || ||||| ||||| || |||||||| || |||||||| || ||||||||||||||||| || ||  | ||| |  
gtcttcatgcttgtggtatcttatatcagactgcccataatcccatactgtccttgtttgaactgtttaatttgacaatt--tgctgtctaatgatttgcagGCTGATCTGTTGGGGAACCCGGTGGTTAGACCAGCTGATATAGAGACAACAGCTCTTGGAGCCGCTTATGCAGCTGGATTAGCAGTGGGGATTTGGACAG

upper sequence: LOC_Os04g55410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv09s0002g07640.t01 (Vitis vinifera), 3'ss of exon 2
ggtgtaattgtagctgtagctta-gtgaaacgtttctctttgcaattgtaaaatctctccaaat-tcccataagatcactgattttgcatgcacacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACTGCCCTTGGAGCTGCGTATGCAGCTGGATTAGCTGTTGGAGTCTGGTCGA
|   | ||  | |  ||| ||||  | | ||    |    | | ||  |    |   |  || | |   ||  ||  | |  |  ||  |    |  ||||||||||| |  |||| | ||| || || ||||| ||||| || |||||||| || |||||||| || ||||||||||||||||| || ||  | ||| |  
gtcttcatgcttgtggtatcttatatcagactgcccataatcccatactgtccttgtttgaactgttttatttgacaatt--tgctgtctaatgatttgcagGCTGATCTGCTGGGGAACCCGGTGGTTAGACCAGCTGATATAGAGACAACAGCTCTTGGAGCCGCTTATGCAGCTGGATTAGCAGTGGGGATTTGGACAG

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|89176392|gb|CI043413.1|CI043413
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|89179779|gb|CI044058.1|CI044058
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|29655940|gb|CB652215.1|CB652215
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|86497148|gb|CI139781.1|CI139781
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|29639143|gb|CB644152.1|CB644152
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|29655885|gb|CB652160.1|CB652160
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|88975521|gb|CI021603.1|CI021603
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|29655941|gb|CB652216.1|CB652216
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|29613287|gb|CB618300.1|CB618300
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|29666025|gb|CB662300.1|CB662300
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTTTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|86496721|gb|CI139354.1|CI139354
EST:     TGCGCGTTGATGGTGGT-CTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|88557574|gb|CI487992.1|CI487992
EST:     TCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|116875030|gb|EC365538.1|EC365538
EST:     TGCGCGTTGATGGTGGTGCTACTGTCGACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|89195097|gb|CI051210.1|CI051210
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|29666024|gb|CB662299.1|CB662299
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|86260040|gb|CI065913.1|CI065913
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|88591302|gb|CI708227.1|CI708227
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|86539728|gb|CI179934.1|CI179934
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|29682347|gb|CB678622.1|CB678622
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
EST: gi|88592993|gb|CI711139.1|CI711139
EST:     TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAG                         GCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT
genomic: TGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACT

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: 73 (upstream exon), 45 (downstream exon)
Score: 10

GGATGCTGGGGAGGCAGGAGAAGTGAAGAGTGCAGAAGGGGAGTTCCTGCTGCGCGTTGATGGTGGTGCTACTGTCAACAATCTTCTCATGCAGATCCAGgtaataatcc ... acacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACTGCCCTTGGAGCTGCGTATGCAGCTGGATTAGCTGTTGGAGTCTGGTCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaaaatctctccaaattcccataagatcactgattttgcatgcacacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACTGCCCTTGGAGCTGCGTATGCAGCTGGATTAGCTGTTGGAGTCTGGTCGA
                             cactgat  putative branch site (score: 10)
                      ataagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgtaattgtagctgtagcttagtgaaacgtttctctttgcaattgtaaaatctctccaaattcccataagatcactgattttgcatgcacacctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACTGCCCTTGGAGCTGCGTATGCAGCTGGATTAGCTGTTGGAGTCTGGTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - -ctgtagc
- - - - - - - - - - - - - - - - - - ctttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgc