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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggaaataatttagggcattgaaaaccattcttcagtaatattacaatcagttttgattttcaactatactaaccaattaagctgcaatgttatatgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCGATGATCCTCGCACCTTGAACAAGACAATATACATAAGACCACAAGATAA

Basic information

species Oryza sativa
transcript LOC_Os12g16220.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G326116_T01 (Zea mays), 3'ss of exon 3
-----aggaaataatttagggcattgaaaacca-ttcttcagtaatattacaatcagttttgattttcaactatactaaccaattaagctgcaatgttatatgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCGATGATCCTCGCACCTTGAACAAGACAATATACATAAGACCACAAGATAA
          |||  |      | | |||     || ||||  || ||||  ||    ||| | |   |  |  | |||  |  || |||          |||||||  | ||    |||||||| ||||| | ||| ||||||||||| ||  | |||||||||||| | |||||||||||| ||||||||||||||| ||| ||
tctttgtatcatagatatccttagtaaaacttggttgttcatcaacattagcat----ttttactaggagatgaattaaata--taggctcatgaccaccatgcagCTATATTCTGTGATGAAGACGATGTTGCAACGTATACAATCAAGTCTGTTGATGATCCTCGCGCATTGAACAAGACACTATACATAAGACCACCAGAAAA

upper sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G17680.1 (Glycine max), 3'ss of exon 2
aggaaataatttagggcattgaaaaccattcttcagtaatattacaatcagttttgattt-tcaactatac---taaccaattaagctgcaatgttata--tgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCGATGATCCTCGCACCTTGAACAAGACAATATACATAAGACCACAAGATAA
     | ||  | || || |   || | ||  |||  |   ||| | |   ||||  | | ||||| | |    ||  || |   ||     ||| ||   ||||||  ||||| |||||||||||||||| | |||||||||||||||  |||| |||||||| || ||| | ||||| ||| | ||| |||| || | ||| ||
-----aaaaccttggccaataccaaac-ttaatcaaaatagttatattttattttattatgtcaacaagatggttagtcattatggcatttctgtgatgattgcagCTATTTTTCTGGATGAAGATGATGTTGCAACATATACAATCAAGGCAATAGATGATCCACGAACCCTTAACAAAACATTGTACCTAAGGCCTCCAGAAAA

upper sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G34470.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------aggaaataatttagggcattgaa---aaccattcttcagtaatattacaatcagttttgattttcaactatactaaccaat--taagctgcaatgttata-tgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCGATGATCCTCGCACCTTGAACAAGACAATATACATAAGACCACAAGATAA
                                                                                     | |  |    |||       ||   |  |||  || |  ||  ||| |  ||    ||    |    | || ||     |  |||      |  | | | |||||   ||| | || ||||||||||||| | | |||| ||||| ||  |||||||||||||||| || |||||||||||  ||||| ||||||||| ||| ||
gtactccacattttaaaaattccaatcaatcataaaacaagtgttagaaagaaagtgtcatagtgtcgttactttctttatatttgtatgtgtcatagtatgcgaaatgtattcatagtttaccaaatttaaacacatgcatgcacatgtggtctaatactttgtactaattaatgaattcacaatgcagTTGTTTATATGAATGAAGATGATGTTGCAGCATACACAATAAAGACAATCGATGATCCTCGAACATTGAACAAGACGGTATACCTAAGACCACCAGAAAA

upper sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0033g00290.t01 (Vitis vinifera), 3'ss of exon 2
aggaaataatt-tagggcattgaaaaccattcttcagtaatattacaatcagttttgattttcaactatactaaccaattaagctgcaatgttatatgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCGATGATCCTCGCACCTTGAACAAGACAATATACATAAGACCACAAGATAA
      || ||  |    |||  |||   || |     ||  | ||  |  |  || ||  |  | |||| |       |    | |   ||  || |||||| |||| ||||||||| ||||| | | |||||| ||||||||| |||| ||||||||||| || |||||||||||| | ||||| || |||| ||| ||
-----gtacttacaattaattataaaattttgtgatacaaattaactctttgcatt-atgatggagtata-tgtgtgcatgttttacggggtattacgcagCGGTTTTCGTGGATGAATATGATATTGCAACATACACAATCAAAACAATAGATGATCCTCGTACTTTGAACAAGACAGTTTACATTAGGCCACCAGAAAA

upper sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0033g00260.t01 (Vitis vinifera), 3'ss of exon 2
aggaaataatttagggcattgaaaaccattcttcagtaatattacaatcagttttgattttcaactatactaaccaattaagctgcaatgtta-----tatgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCGATGATCCTCGCACCTTGAACAAGACAATATACATAAGACCACAAGATAA
    || ||||| |    |        | |      ||   ||| |||| |  |  |||| |||      | |  || |  |||    || |      |||| |||  |||||||||| ||||||||||| | | |||| || |||||| |||| ||||||||||| ||  ||||||||||| | ||| | || |||| ||| ||
---taacaattttgaagttgtttttatactgagacatagggtta-aatccgcatacattt-caatggagttcattaaatgtgcttgtttggtggatactatgtagCTGTTTTTGTGGACGAAGATGATGTTGCAGCATACACGATCAAAGCAATAGATGATCCTCGTACACTGAACAAGACAGTCTACGTTAGGCCACCAGAAAA

upper sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv17s0053g00460.t01 (Vitis vinifera), 3'ss of exon 2
aggaaata-atttagggcattgaaaaccattcttcagtaatattacaatcagttttgattttcaactatactaaccaattaagctgcaatgttatatgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCGATGATCCTCGCACCTTGAACAAGACAATATACATAAGACCACAAGATAA
      || ||  |    |||  |||   || |     ||  | || ||  |  || ||  |  | |||| ||      |    | |   ||  || |||||| |||| ||||||||| ||||| | | |||||| ||||||||| |||| ||||||||||| || |||||||||||| | ||||| || ||||  || ||
-----gtacatacaattaattataaaattttgtgatacaaattaactatttgcatt-atgatggagtata-tatgtgcatgttttacggggtattacgcagCGGTTTTCGTGGATGAATATGATATCGCAACATACACAATCAAAACAATTGATGATCCTCGTACATTGAACAAGACAGTTTACATTAGGCCACCGGAAAA

upper sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0033g00270.t01 (Vitis vinifera), 3'ss of exon 2
aggaaataatttagggcattgaaaaccattcttcagtaatattacaatcagttttgat----tttcaactatactaaccaattaagctgcaatgttatatgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCGATGATCCTCGCACCTTGAACAAGACAATATACATAAGACCACAAGATAA
      || ||      | | | ||  ||| |    ||  | |  ||| | ||   ||    ||     ||||  ||||  ||    | |   ||  ||| ||||| |||| ||||||||||||||||| | ||||||  |||||||| |||| ||||||||||| || |||||||||||| | ||||| ||||||| ||| ||
-----gtacttacaattaattataaa-attttgtgatacaact-taattatttgcaatacgattgtgtgtatatgaaccggtt---ttacggggtattatacagCGGTTTTCGTGGATGAAGATGATGTTGCAACATACGCAATCAAAACAATAGATGATCCTCGTACATTGAACAAGACAGTTTACATCAGACCACCAGAGAA

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|25804366|gb|CA760327.1|CA760327
EST:     CCTCCCTCCCAAAGAGAGAGCTAATGTGTATGGGGATGGTAACGTCAAAG                         CGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCG
genomic: CCTCCCTCCCAAAGAGAGAGTTAATGTGTATGGGGATGGTAACGTCAAAGgtaaaaaagt ... ttatatgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCG
EST: gi|29660598|gb|CB656873.1|CB656873
EST:     CCTCCCTCCCAAAGAGAGAGTTAATGTGTATGGGGATGGTAACGTCAAAG                         CGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCG
genomic: CCTCCCTCCCAAAGAGAGAGTTAATGTGTATGGGGATGGTAACGTCAAAGgtaaaaaagt ... ttatatgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCG
EST: gi|702642|gb|D48933.1|D48933
EST:     CCTCCCTCCCAAAGAGAGAGTTAATGTGTATGGGGATGGTAACGTCAAAG                         CGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCG
genomic: CCTCCCTCCCAAAGAGAGAGTTAATGTGTATGGGGATGGTAACGTCAAAGgtaaaaaagt ... ttatatgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCG
EST: gi|29660599|gb|CB656874.1|CB656874
EST:     CCTCCCTCCCAAAGAGAGAGTTAATGTGTATGGGGATGGTAACGTCAAAG                         CGTTTTTTGTGGATGAAGATGATGTGGGAACATATCCAATCAAATCAATCG
genomic: CCTCCCTCCCAAAGAGAGAGTTAATGTGTATGGGGATGGTAACGTCAAAGgtaaaaaagt ... ttatatgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCG
EST: gi|25799331|gb|CA755292.1|CA755292
EST:     CCTCCCTCCCANAGAGAGAGTTAATGTGTATGGGGATGGTAACGTCAAAG                         CGTTTTTTGTGGATGAAGATGATGT
genomic: CCTCCCTCCCAAAGAGAGAGTTAATGTGTATGGGGATGGTAACGTCAAAGgtaaaaaagt ... ttatatgcagCGTTTTTTGTGGATGAAGATGATGT

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: 74 (upstream exon), 73 (downstream exon)
Score: 29

AACTGCTTTGCTGCTTACTTCTGTCCTAATCTCAGCCAGCTGACCTCCTTCCTCCCTCCCAAAGAGAGAGTTAATGTGTATGGGGATGGTAACGTCAAAGgtaaaaaagt ... ttatatgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCGATGATCCTCGCACCTTGAACAAGACAATATACATAAGACCACAAGATAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcagttttgattttcaactatactaaccaattaagctgcaatgttatatgcagCGTTTTTTGTGGATGAAGATGATGTGGGAACATATACAATCAAATCAATCGATGATCCTCGCACCTTGAACAAGACAATATACATAAGACCACAAGATAA
                      tactaac  putative branch site (score: 29)
      ttttgatttt  TA-rich tract