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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctagtatagccctttcttcatattcctttagttgctttcaggcaaaagaatactttgttttatgcttaatttagttatttcttgaacctgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG

Basic information

species Oryza sativa
transcript LOC_Os01g52640.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52640.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G079904_T01 (Zea mays), 3'ss of exon 5
------ttctagtatagccctttcttcatattcctttagttgctttcaggcaaaagaatactttgttttatgcttaatttagttatttcttgaacctgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG
       |  |||     || |||  | | || ||||    |||   ||||| | |     ||  ||   ||  | ||||| ||||||  | ||| | ||   ||||| || ||||| ||||| |||||||| |||||||||||||||||||| || |||||||||
acgtgtatacagtggttacccttcagc-tgttgctttctgcgctgaaaggcacatgt---tttcattgagtggctgatttacttatttggtaaacatcttc--cagAACTTCGTTGGCCTTTCCATATCTGACGGTTACATTGCTACTGGCTCTGAAACAAATGAG

upper sequence: LOC_Os01g52640.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G061602_T01 (Zea mays), 3'ss of exon 5
ttctagtatagccctttcttcat---attcctttagttgctttcaggcaaaagaatactttgttttatgcttaatttagttatttcttgaacctgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG
 |  |  |||||| ||| |  |     || ||||   ||||   |||||     ||  ||  ||   || |  ||||| |||||| || ||||| |||  ||||| || ||||| ||||| ||||||||||||||||||||||||||||| || |||||||||
-tgcaacatagccttttgtatagtgagttgctttctgtgctgaaaggcactgatat-tttcattgggtgatcgatttacttattttttaaaccttttgc-cagAACTTCGTTGGTCTTTCCATATCTGATGGTTACATTGCTACTGGCTCTGAAACAAATGAG

upper sequence: LOC_Os01g52640.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G25240.1 (Glycine max), 3'ss of exon 7
ttctagtatagccctttcttcatattcctttagttgctttcaggcaaa---agaatactttgttttatgct-taatttagttatttcttgaacctgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG---------------------
      |  |    ||    ||| |    ||| || ||   |     |   |   || ||   ||| |||   ||| |  | ||        | | |    |||||||| || ||  | ||| ||||||||||||||||||||||||| ||||||||||| |||                     
----tatgcaaaatttgggccatttgtaattaattactgcaaattttatatatggtatttaaatttctgcggcaatatgatgatgcaccttccttttgttgcagAATTTCGTGGGGTTGTCTGTATCTGATGGTTACATTGCTACTGGTTCAGAGACAAACGAGGCATTTCATTTTTCCTCTCTC

upper sequence: LOC_Os01g52640.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G35320.1 (Glycine max), 3'ss of exon 7
----ttctagtatagccctttcttcatattccttta-gttgctttcaggcaaaagaatactttgttttatgcttaatttagttatttcttgaacctgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG
     | || |||     |     ||| ||  | || |    |||             ||  |    ||| ||     |   | || |||     |||    ||||| ||||| ||  | ||  ||||||||||||||||||| ||||| |||||||||||||||
gctcatttattatcaatttccaaacatttttatgtaagccatttttcaattttgaggaaccatagaatatcctgctgatgcatcttcctt-----tgtcttgcagAACTTTGTGGGGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAG

upper sequence: LOC_Os01g52640.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G35190.1 (Glycine max), 3'ss of exon 10
ttctagtatagccctttcttcatattcctttagttgctttcaggcaaaagaatacttt----gttttatgcttaatttagttatttcttgaacctgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG
    ||  |      || || || | | |  | ||   |  | || |      | |||    || | ||     ||   | |  | | |   ||| |    ||||| ||||| ||  | ||  ||||||||||||||||||| ||||| |||||||||||||||
----aggctcaattattattgatttccatacatttttatgtaagccatttttcaattttgaggtatcatataatatcctgctgatgcatcttcctttcttgcagAACTTTGTGGGGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAG

upper sequence: LOC_Os01g52640.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv19s0014g02660.t01 (Vitis vinifera), 3'ss of exon 6
ttctagtatagccctttcttcatattcctttagttgctttcaggcaaaagaatactttgttttatgcttaattta--gttatttcttgaacctgttga-acagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG
    |||  |  | | |  |  | ||| | || |   |    |   ||| |   ||||| ||||||  |  |||   | |  |   ||  |   |||   ||||| ||||| ||  | ||| |||| ||||||||||||||||| ||||||||  ||||||||
--tcagttcaaacgtgtgatt-ttttcatgtattaattcattgttgaaatatgcctttggtttatgtatgttttgttgctgatgtatgttctccttgttgcagAACTTTGTAGGTTTGTCTGTATCCGATGGTTACATTGCTACGGGCTCAGAAGCAAATGAG

upper sequence: LOC_Os01g52640.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv12s0028g03570.t01 (Vitis vinifera), 3'ss of exon 6
--ttctagtatagccctttcttcatattcctttagttgctttcaggcaaaagaatactttgttttatgcttaatttagttatttcttgaacctgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG
   | |||| ||    | |       | |  || |    |    |   |   ||  ||||||||  |  || || || | ||   ||   | || |   ||||||||||| || || |||||||||||||| ||||||||||| ||||||||||||||||||
ttctttagtgtactaatcttggtgattgcaatttgagaatgatggagtagcaaacgctttgtttgtttgttcatcta-taatacgttttccttggttt-cagAATTTTGTGGGTCTATCTATATCTGATGGATACATTGCTACGGGCTCAGAGACAAATGAG

upper sequence: LOC_Os01g52640.3 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ26072 (Selaginella moellendorffii), 3'ss of exon 7
ttctagtatagccctttcttcatattcctttagttgctttcaggcaaaagaatactttgttttatgcttaatttagttatttcttgaacctg-----ttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG
                                              |  || |   ||    |||  |    |   |||  || ||||||       |||| |||||||| |||||||| ||| |||| ||||| ||||| ||   |||||||||||||||||  
--------------------------------------------gtagcgactctctttcgatatcttcgtgtctcttacgtcgtgaaccgacttgcttgagcagAATTTCGTTGGACTGTCTGTATCCGATGGCTACATCGCGTGTGGCTCAGAGACAAATGCT

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|29668762|gb|CB665037.1|CB665037
EST:     GGATAATTGACAGTCCGCTTCGGACATTTACAGGTCATACAAACACTAAG                         AATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAG
genomic: GGATAATTGACAGTCCGCTTCGGACATTTACAGGTCATACAAACACTAAGgttagaatat ... tgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAG
EST: gi|29668796|gb|CB665071.1|CB665071
EST:     GGATAATTGACAGTCCGCTTCGGACATTTACAGGTCATACAAACACTAAG                         AATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAG
genomic: GGATAATTGACAGTCCGCTTCGGACATTTACAGGTCATACAAACACTAAGgttagaatat ... tgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAG
EST: gi|29685395|gb|CB681670.1|CB681670
EST:     GGATAATTGACAGTCCGCTTCGGACATTTACAGGTCATACAAACACTAAG                         AATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAG
genomic: GGATAATTGACAGTCCGCTTCGGACATTTACAGGTCATACAAACACTAAGgttagaatat ... tgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAG

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: 70 (upstream exon), 60 (downstream exon)
Score: 28

ATCTACTGACAACTCCTTGAAGCTCTGGGACTTGTCCATGAGTCAGGCAAGGATAATTGACAGTCCGCTTCGGACATTTACAGGTCATACAAACACTAAGgttagaatat ... tgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagaatactttgttttatgcttaatttagttatttcttgaacctgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG
                    gcttaat  putative branch site (score: 28)
          tttgttttatgcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctagtatagccctttcttcatattcctttagttgctttcaggcaaaagaatactttgttttatgcttaatttagttatttcttgaacctgttgaacagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG

- - - - - - - - - - - - - - - - gttgctt
- - - - - - - - - - - - - - - - - - - - caggcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcttg