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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggagtgttagtttcgaatatctgtatatagccattgacagagaattcgtttctgttattattacctgatattgttgttcttcttgtgttatcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG

Basic information

species Oryza sativa
transcript LOC_Os06g48300.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 1
gggagtgttagtttcgaatatctgtatatagccattgacagagaattcgtttctgttattattacctgatattgttgttcttcttgtg--ttatcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG
  || | |   |       ||  || | |    ||       |  ||  |   || |   || |  |||| |||   |  || || ||  || | |   ||||   ||||| ||||| |||||||| ||||| ||||| ||||| || ||||| || ||||| || || ||||| || | |||||||||||| ||||| || 
-agattatagatgattttaattggtttttctttat-atttctgggtttttagttgattgaatgatatgattttgacatgtttgttatgatttgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA

upper sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 2
gggagtgttagtttcgaatatctgtat--atagccattgacagagaattcgtttctgttattattacctgatattgttgttcttcttgtgttatcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG
  || ||||  | | |  |     |||   |   ||   ||  |  | |     |   |   || |     |      |||  | |||  || |  | | |||   ||||| ||||| ||||| || ||||| ||||||||||| || ||||| || ||||| || || ||||| || |||||||||||||| || || || 
atgattgtttctcttgtgttatcatatcggtgagcaaaaactaaagaatgaggccgcatgagatgatt--gtgacacagtttgttttgatttgtatttatagTCACAATGGAAAATTCAGCTACGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGAAGGTGAA

upper sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 1
--gggagtgttagtttcgaatatctgtatatagccattgacagagaattcgtttctgttattattacctgatattgttgttcttcttgtgttatcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG
      |  ||   ||  || |     | | ||  |   ||  |  | |         |   || |     |      |||  | |||  || |  | | |||   ||| | ||||| |||||||| ||||| ||||||||||| || ||||| || ||||| || || ||||| || |||||||||||||| ||||| || 
tctctggcatttcctttaaaaaaaaaaagaaagaaaaaaactaaacaatgaagctgcatgagatgatt--gtgacacagtttgttttgaattgtatttatagTCACAATAGAAAATTCAGCTATGGGTATGCTAGCTCTCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAGAATTGATGGTGTTGATGGTGAA

upper sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G12220.2 (Glycine max), 3'ss of exon 1
---------------gggagtgttagttt-cgaatatctgtatatagccattgacagagaattcg---tttctgttatt---attacctgatattgttgttcttcttgtg--ttatcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG
                | | |   || ||    ||   | ||  | |   ||         |  |   |||  |||  |   || |  |||| |||   |  || || ||  || | |   ||||   ||||| ||||| |||||||| ||||| ||||| ||||| || ||||| || ||||| || || ||||| || | |||||||||||| ||||| || 
gtgatttatgtgtgcagaattcaaagattatagatgattttaattggtttttctttatatttctgggtttttagttgattgaatgatatgattttgacatgtttgttatgatttgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA

upper sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 2
gggagtgttagtttcgaatatctgtatatagccattgacagagaattcgtttctgttatt--attacctgatattgttgt------tcttcttgtgttatcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG
           ||    ||   | ||  | |   ||     | | |||  |  | ||| |  |||   ||||||| || |      |  | |||  || | |   ||||   ||||| ||||| |||||||| ||||| ||||| ||||| || ||||| || ||||| || || ||||| || | |||||||||||| ||||| || 
--------agattatagatgattttaattggtttttcttttatatttctgtctttttagttgattgaatgatattattttaacatgttgttttgaattgtaactgcagTCAGAATGGAAAATTCAGCTATGGGTATGCTAGCTCCCCTGGCAAGAGATCTTCAATGGAAGATTTTTATGAGACAAAAATTGATGGTGTTGATGGTGAA

upper sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 2
gggagtgttagtttcgaatatctgtatatagccattgacagagaattcgtttctgttattattac--ctgatattgttgttcttcttgtgt----tatcatg-acagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG
    |||| | | |   || | ||   || | |||         |   ||  ||||   |  | |  ||| |  | ||  | ||  ||       ||  ||| |||||   || || || || |||||||| ||||| |||||||| || |||||||| || ||||||||||||||||| || || || || || || || || || 
----gtgtgattat---atgtttgcgcattggcatcattcctagaaatgtgactgtagatgctgctgctgctgctattaattttaatgaacactctaatatgtacagTCAGAACGGGAAGTTCAGCTATGGATATGCAAGCTCTCCCGGTAAAAGATCTTCTATGGAGGACTTCTATGAAACTAGGATCGACGGCGTTGAAGGGGAA

upper sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G24940.1 (Arabidopsis thaliana), 3'ss of exon 1
----gggagtgttagtttcgaatatctgtatatagccattgacagagaattcgtttctgttattattacctgatattgttgttcttcttgtgttatcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG
         |||| ||||||  |    |  ||||   |||    ||   |||||||   |||  || | || ||     ||||  |    | ||   |   ||||   ||||| |||||||||||||| ||||| |||||  |||||||||| || || ||||| ||||| | ||| || || || || ||| |||||||||| 
ctagctacatgtttgtttcgtctcaaagattatattgattc---gaactttcgttttccttaacatgaactcatcacaatgtttatgaacttttga-actgcagTCAGAATGGAAAATTTAGCTATGGATATGCAAGCTCAGCTGGAAAAAGGTCATCTATGGAAGACTTTTTTGAGACAAGGATCGACGGTATCGATGGAGAA

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|33680920|gb|CF309159.1|CF309159
EST:     GGGCTCGCCGGAGAGGCCGCTGGCTCGCCTGGCAGTGGCGGCGGGTTCAG                         TGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATC
genomic: GGGCTCGCCGGAGAGGCCGCTGGCTCGCCTGGCAGTGGCGGCGGGTTCAGgtattccgtt ... atcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATC
EST: gi|218482423|gb|FG960534.1|FG960534
EST:     GGGCTCGCCGGAGAGGCCGCCGGCTCGCCTGGCAGTGGCGGCGGGTTCAG                         TGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGACAAACGAT
genomic: GGGCTCGCCGGAGAGGCCGCTGGCTCGCCTGGCAGTGGCGGCGGGTTCAGgtattccgtt ... atcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAA-GAT
EST: gi|88391402|gb|CI598220.1|CI598220
EST:     GGGCTCGCCGGAGAGGCCGCTGGCTCGCCTGGCAGTGGCGGCGGGTTCAG                         TGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATC
genomic: GGGCTCGCCGGAGAGGCCGCTGGCTCGCCTGGCAGTGGCGGCGGGTTCAGgtattccgtt ... atcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATC
EST: gi|88377052|gb|CI597836.1|CI597836
EST:     GGGCTCGCCGGAGAGGCCGCTGGCTCGCCTGGCAGTGGCGGCGGGTTCAG                         TGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATC
genomic: GGGCTCGCCGGAGAGGCCGCTGGCTCGCCTGGCAGTGGCGGCGGGTTCAGgtattccgtt ... atcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATC
EST: gi|218481440|gb|FG958928.1|FG958928
EST:     GGCTCGCCGGAGAGGCCGAC-GGCTCGCCTGGCAGTGGCGGAGGGTTCAG                         TGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATC
genomic: GGCTCGCCGGAGAGGCCG-CTGGCTCGCCTGGCAGTGGCGGCGGGTTCAGgtattccgtt ... atcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATC
EST: gi|66913181|gb|CX100029.1|CX100029
EST:     GGGCTCGCCGGAGAGGCCGCCGGCTCGCCTGGCAGTGGCGGCGGGTTCAG                         TGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATC
genomic: GGGCTCGCCGGAGAGGCCGCTGGCTCGCCTGGCAGTGGCGGCGGGTTCAGgtattccgtt ... atcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATC
EST: gi|33682770|gb|CF311009.1|CF311009
EST:     GGGCTCGCCGGAGAGGCCGCTGGCTCGCCTGGCAGTGGCGGCGGGTTCAG                         TGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATC
genomic: GGGCTCGCCGGAGAGGCCGCTGGCTCGCCTGGCAGTGGCGGCGGGTTCAGgtattccgtt ... atcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATC

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: 65 (upstream exon), 65 (downstream exon)
Score: 9

TCTCGCAGGGAGCGGAGGAGGAGGAGGACGACGGCGAGGTGCGCTTGATGGGGCTCGCCGGAGAGGCCGCTGGCTCGCCTGGCAGTGGCGGCGGGTTCAGgtattccgtt ... atcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtttctgttattattacctgatattgttgttcttcttgtgttatcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG
                  acctgat  putative branch site (score: 9)
     ttctgttattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggagtgttagtttcgaatatctgtatatagccattgacagagaattcgtttctgttattattacctgatattgttgttcttcttgtgttatcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - ttctgtt