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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatgtctcaacctgctatagttcttgcattttcaccatgaatcaattcgtgatgcatcatcccggttcatatctgatagtattgttttcatatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA

Basic information

species Oryza sativa
transcript LOC_Os04g42840.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 20
---------------------aaatgtctcaacctgctatagttcttgcattttcaccatgaatcaa---ttcgtgatgcatcatcccggttcatatctgatagtattgttttcatatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA
                          |  ||   | || ||| |   |   |||    ||   |  |   ||| | || |||    |   |  |  | |  | ||    ||||  |   | ||||||||||| |||||  |||||||||||||||||||||||||||| ||||| |  || || ||||||||||||| |||||||||||| ||||| ||||| |
gtcagtaccatcatattttccttgctttgcattattctgtaggtaccgaccttttcttatatcttgaaatttcataatacattgctctaatg-acttatccttgtcaaattttttttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTTGCTCCATACTTGGAAGGGCTTAGCAGCACGCAGCTCCGCCTAGTAACCA

upper sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 20
------aaatgtctcaacctgctatagttcttgcattttcaccatgaatcaattcgtgatgcatcatcccggttcatatctgatagtattgttttcatatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA
       ||  | |   | |||| | | | |    ||||| ||||     |||| |   |   ||||     |||  || | ||  || || |   ||  |   |||| ||||| |||||  | |||||||| || |||||||||||||| |||||  | || ||||||||||| ||||||||||| ||| ||    | || || |
ttgctagaaattgtgggcatgcttttgctgtcat-ttttctccattctcaaatttggtctctttcatt---attctcattttatgttaatggtgg-atggtac-agACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTTTTGCCATATTTGGAAGGACTTAACAGCACACAGTTGAAGTTGGTCACCA

upper sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 20
-aaatgtctcaacctgctatagttcttgcattttcaccatgaatcaattcgtg-atgcatcatcccggttcatatctgatagtattgttttcatatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA
  |   |       |  | ||   ||   | ||  |   |   ||  ||  |  || |    ||    | | ||| | |||  | |||    ||  ||  |||| ||||| |||||  | |||||||| || |||||||||||||| |||||| | || |||||| |||||||||||||||| ||| ||    | || || |
agaggattagggtattatttatcactaataattatatttttgttccctttatatattctgtttcattatacttattttatataaatgtgg--attgttacagACCGTTGTTTTCTGTCTCGTGGATATTTATATCATGCTTGGGAAAGCATTCTTGCCATATTTGCAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA

upper sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 20
aaatgtctcaacctgctatagttcttgcattttcaccatgaatcaattcgtgatgcatcatcccggttcatatctgatagtattgttttcatatttt-tagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA
 | ||    ||  || |    | |||    | | |   |    || |||   |    |  ||        | ||| ||  | ||  |     ||  |  |||| ||||| |||||  | |||||||| || |||||||||||||| |||||  | || ||||||||||||||||||||||| ||| ||    | || || |
-attgctataaattgttggcatgcttttgctgtaatttttctccatttccataactgttctcttttcatttttctcattttgttaatggtgcatggtacagACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTTTTGCCATATTTGGAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA

upper sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA03G32710.1 (Glycine max), 3'ss of exon 20
aaatgtctcaacctgctatagttcttgcattttcaccatgaatcaattcgtgatgcatcatcccggttcata--tctgatagtat-tgttttcatattttta--gACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA
    || | |     |  || |  ||  |||||   |     |   |||    |  || || | | |||||   ||| ||  ||| |   | |  ||| |||  ||| ||||| |||||  | |||||||| || |||||||||||||  |||||| | || |||||| |||||||||||||||| ||| ||    | || || |
----gtattatttatcactaataattatatttttgtctgtcctttgttccctttatat-attctgtttcattattcttattttatgtaaatgcggattgttacagACCGTTGTTTTCTGTCTCGTGGATATTTATATCATGCTTGGGAGAGCATTCTTGCCATATTTGCAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA

upper sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 20
lower sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 20
-----------------aaatgtctcaacctgcta-tagttcttgcattttcaccatgaatcaattcgtgatgcatcatcccggttcatatctgatagtattgttttcatatttt-tagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA
                 |||    | |   | ||| |  | |  | |  ||     |  || || | | ||    | ||  |      | | |||  |  |  ||    | | ||  |||| || || |||||  | || || || || || ||||||||||| |||||  | |||||||||||||| || |||||||||||| | || || || || |
gtaaaggaattgaaaaaaaaaacttgacttttctactcataccagtaacttacgatttgatgaaattg-gacaagttataactaactctctatgagggggtctttgctgtttgttgcagACAGTGGTGTTCTGTCTAGTAGACATATATATAATGCTTGGGAAAGCATTTTTGCCGTATTTGGAAGGTCTAAACAGCACGCAGGTTCGTCTAGTGACCA

upper sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 20
lower sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 17
----aaatgtctcaacc-tgctatagttcttg-cattttcaccatgaatcaattcgtgatgcatcatcccggttcatatctgatagtattgttttcatatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA
    | ||| |  |    ||||  | | | ||  ||| |  | ||| ||  |||  |  |   | ||   |    ||||    |  | |||  |   | ||   ||||||||||||||||  | ||||| ||||| |||||||||||||| || ||  | || ||  |||| |||||||||||||| ||  ||||  | || || |
catcatatgacaaagttgtgcttaaatacatgatattctacctatgcatgcatttatatt---ttattttg---tatattgatttattttgagtctgtgttggcagACTGTTGTATTCTGTCTAGTGGACATCTATATCATGCTTGGGAAAGCTTTTTTGCCATACCTGGAGGGGCTTAACAGCACACAATTGCGGTTGGTGACGA

upper sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 20
lower sequence: EFJ13050 (Selaginella moellendorffii), 3'ss of exon 14
aaatgtctcaacctgctatagttcttgcattttcaccatgaatcaattcgtgatgcatcatcccggttcatatctgatagtattgttttcatatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA
                                          ||      | | |  || ||||  |   |   |  ||  |||  || || |      ||||||||| || ||||||||||| |||||||||   || || || ||||||||||||||| ||    | || | |||||  ||| | || || || || |
-----------------------------------------gtctgggtttaaagt-tcctccctttcggtgcttcttatgatttcttccaca------gACTGTTGTCTTTTGCTTGGTGGACATCTACATCGCACTCGGAAAAGCATTCGTCCCGTATCTGAGCAGCCTCAGCAGCAACCAGTTACGGCTGGTCACGA

upper sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 20
lower sequence: EFJ14058 (Selaginella moellendorffii), 3'ss of exon 14
aaatgtctcaacctgctatagttcttgcattttcaccatgaatcaattcgtgatgcatcatcccggttcatatctgatagtattgttttcatatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA
                                       |  |  |||     |   || ||||  |   |   |  ||  |||  || || |      ||||||||| || ||||||||||| |||||||||   || || || ||||||||||||||| ||    | || | |||||  ||| | || || || || |
---------------------------------------gtctggatttaaagt---tcctccctttcggtgcttcttatgatttcttccaca------gACTGTTGTCTTTTGCTTGGTGGACATCTACATCGCACTCGGAAAAGCATTCGTCCCGTATCTGAGCAGCCTCAGCAGCAACCAGTTACGGCTGGTCACGA

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|29626001|gb|CB631012.1|CB631012
EST:     TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAG                         ACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
genomic: TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
EST: gi|38478559|gb|CF962692.1|CF962692
EST:     TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAG                         ACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
genomic: TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
EST: gi|58682357|gb|CK071044.1|CK071044
EST:     TGCCAGCACTGTTTGATGCTTTTAGTAACCGAAGCCCTGATGTTCGAAAG                         ACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
genomic: TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
EST: gi|14981910|gb|BI306588.1|BI306588
EST:     GTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAG                         ACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
genomic: GTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
EST: gi|88372765|gb|CI612693.1|CI612693
EST:     TGGCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAG                         ACTGTTGTATTCTGTTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
genomic: TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
EST: gi|86902991|gb|CI324461.1|CI324461
EST:     TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAG                         ACTGTTGTATTCTTCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
genomic: TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC

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), 47 (downstream exon)
Score: 6

TGTTGGACGGCTTTCCGAGGAGGAATTGATGAATCAGTTGCCCACATTTTTGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcgtgatgcatcatcccggttcatatctgatagtattgttttcatatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA
                          atctgat  putative branch site (score: 6)
                                        ttttcat  putative PPT
                               atagtattgttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatgtctcaacctgctatagttcttgcattttcaccatgaatcaattcgtgatgcatcatcccggttcatatctgatagtattgttttcatatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - -cctgcta
- - - - - - - - - - - tcttgca
- - - - - - - - - - - - - - - - - - catgaat
- - - - - - - - - - - - - - - - - - - - - - - - - tgatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcccg