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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcacaacttcttgccataaagcagtgaattcactgttaatcatctaaataacaagttggatcatctttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA

Basic information

species Oryza sativa
transcript LOC_Os10g33680.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
gtgatcacaacttcttgccataaagcagtgaattcactgttaatcatctaaataacaagttggatcatctttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
||||| | || | |||   ||||| |  |  |||  |||  ||  ||  |  |||  | |||| | || |||  |||  |||||||||||||||||||| |||| |||||||| ||||| ||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||
gtgattataa-tcctta--ataaa-ctttagatttgctgccaagtattaagttaaataattggctaatgttta-attgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 11
gtgatcacaacttcttg---ccataaagcagtgaattcactgttaatcatctaaataa---caagttggatcatc--tttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
|| |  | ||  |   |   | |||   |    |||| |   ||| | |||| |  ||   |   ||  | ||    | |||  || ||||||||||  |||||| ||| || ||||||||||| || ||||||||||||||||||||  | ||||||||||||||||||||||||   |||||||  |
gtaaaaataagattgagatcctatatcactaacaattaaggcttagtaatcttagcaagttctgattacaacaagggtattttgtttagGAACGTGAGGATCCAAATTTGACAGAGTGGGATCGTTTTGCACATAGAGAGTATATTAGGCTTTCCATGGAAGAAGATGGTGAAGATATGTCAAATGCCA

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 11
----------------------gtgatcacaacttcttgccataaagca-gtgaattcactgttaatcatctaaataacaagttggatcatctttttattt---cagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
                       | ||  ||   |   |  |  | | | |       ||||||| | |  |   |   || | | ||     | || | |    |||||||||| || ||||| || || ||||||||||| || || ||| |||| ||||||||  | || |||||||||||||  |||||||| || |||||||
gtgcatgaaatatttgataaaatttattgcattcttgagttagtatgtatgcttggctactgttagtgacttccttggtaattggtatgcatatcttgtgtgaatagGAACGTGAGAACCCAACATTGACAGAGTGGGATCGATTTGCTCATCGAGAATATATTAGGCTTTCAATGGAAGAAGATGTAGAAGATGCCTCTAATGGAA

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 11
---------------gtgatcacaacttcttgccataaag-cagtg-aattcactgttaatcatctaaat-aacaagttggatcatctttttattt---cagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
                | |        |  |||  |  || ||||   ||| ||| ||  |  |     |  ||    | | |     | || | |   ||||||||||| ||||| || || || ||||||||||| || || |||||||| ||||||||  | || |||||||||||||  || ||||| || || || |
gtgcatgaatatttgataaaagtgttattgtgctgttgagtcagtatgattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G35090.1 (Glycine max), 3'ss of exon 11
gtgatcacaacttcttg---ccataaagcagtgaattcactgttaatcatctaaataa---caagttggatcatc--tttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
|| |  | ||  |   |   | |||   |    |||| |   ||| | || | | |||   |   ||  | ||    | |||  || ||||||||||  |||||| ||| || ||||||||||| || ||||||||||||||||||||  | ||||||||||||||||||||||||   |||||||  |
gtaaaaataagattaagatcctatatcactaacaattaaggcttagtaatgttagtaaattctgattacaacaagggtattttgtttagGAACGTGAGGATCCAAATTTGACAGAGTGGGATCGTTTTGCACATAGAGAGTATATTAGGCTTTCCATGGAAGAAGATGGTGAAGATATGTCAAATGCCA

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 11
---gtgatca-caacttcttgccataaagcagtgaattcactgttaatcatctaaataacaagttggatcatctttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
    | |||| | | ||         |     | |   |||    |  | ||| | |||||  |   ||  ||         ||||| || || || || || || || || ||||| || || ||||||||||||||||||||  | || ||||||||||||| ||||||||| || |||||||
gtactaatcatctaatttaccttgctacttcttcacaccaccac-atgcgtctta-taacatttctaat-gtcaaacggaaacagGAGCGAGAGAACCCTACATTGACAGATTGGGACCGTTTTGCACATAGAGAGTATATTAGGCTATCAATGGAAGAAGATGTTGAAGATGCATCTAATGGAA

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G03960.2 (Arabidopsis thaliana), 3'ss of exon 11
--------------------------------------------------------gtgatcacaacttcttgccat-----aaagcagt--gaattcactgttaatcatctaaata--acaagttggatcatcttt--ttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
                                                          ||  |  |||||||   |      || |||||  | | |   |   | | |   || ||  ||||||   ||  |||||  ||  |  ||||||| ||| |||||| ||| || ||||||||||| || || || |||||||||   |||||||| ||||| |||||||  || || |  |||||||| |
gtaagtttggcttaccagtggagtttttatagcactcaagagggaaaaaaataacaaagaatatgacttcttttaactgctaaaggcagtttgtagtagttcggattgaggcaattagaacaagtataattctctttcattgctgtagGAACGGGAAGATCCAAATTTGACAGAGTGGGATCGATTTGCTCAGAGAGAGTATGCGAGATTGTCAATGGAGGAAGATGTAGATGAAGTCTCAAATGGGA

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgatcacaacttcttgccataaagcagtgaattcactgttaatcatctaa------ataacaagttggatcatctttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
||  |         |||  ||  | |  ||   |     | |  ||           ||||||  |   ||  ||     |   ||||| || || || || || || || || ||||| || || |||||||||||||||||| |  | || ||||||||||||| ||||||||| || |||||||
gtactactccacgtttgatattcaaccttgctgttttcttgacacaatgggcctcttataacatttcaaat-gtcaaacgaaaacagGAGCGCGAGAACCCGACATTGACAGACTGGGACCGTTTTGCACATAGAGAGTATATTCGGCTATCAATGGAAGAAGATGTTGAAGATGCATCCAATGGAA

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgatcacaacttct------tgccataaagcag--tgaattcactgttaatcatctaaataacaagttggatcatctttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
|| |||||||  | |      | || ||||||    |  |   |||  ||   || |  ||  |    ||  | ||   |       |||| || | |||||| || |  || ||||||||||| || || |||||||| ||||||||  | || |||||||||||||  ||||||||||| |||||||
gt-atcacaaaatatagtaaataccttaaagctagctatacatacttatagagatattcatttctcaatgattgattgctgatacatagGAGCGCGCAAATCCGACATGGACAGAGTGGGATCGTTTTGCTCATAGAGAATATATTAGGCTATCAATGGAAGAAGATGTCGAAGATGCTTCTAATGGAA

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 12
--------------gtgatcacaacttcttgccataaagcagtg--aattcactgttaatcatctaaataaca-agttggatcatc--tttttattt------cagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
               | ||     || || |  || || || ||  || |     || ||    | |  |  | |||     |||     |||||||      |||||||| ||  |||||||||| || |||||||| || || ||||||||||| || |||||  | || ||||||||||||||||||||||  ||||||||||
gtaaattcaacatttttataggtgctcctagtaatcaatcattgccaagttgtattttattcctttagcattatagtattcccattggcatttatttggcaagcagGAACGAGAGGATCCAACTTTGACAGAGTGGGACCGCTTTGCACATAGAGAATACATTAGGCTTTCAATGGAAGAAGATGGTGAAGATGTCTCAAATGGAA

upper sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------------------------------------gtgatcacaacttcttgccataaagcagtgaattcactg--ttaatcatctaaataacaagttggatcatct------ttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
                                                         || | |  | |  |    || |   | || ||| | ||  || |    |||  ||| |  || ||  |  |      |||| ||| ||||| | ||| |||| |||||||| || |||||||| || ||||| |  ||||| ||| ||||||| |||||||||||||                     
gtaatgaatttgacaacattttttgtgcttccaacattttgatttattgttgttacatgttgattattgatgaatattagcaattgcatttattggtttgacttgctacttaatacttttgaaaacttgtttgattttgttttagGAAAGGGAAGATCCTACTTTAACTGAATGGGATCGATTTGCACACACTGAGTACATTCGATTGTCTATGGAAGAAGATG---------------------

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|3767272|gb|AU031382.1|AU031382
EST:     TCAACAAATTTATNGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAG                         GANCGTGAAAATCCAACTTTAACCG
genomic: TCAACAAATTTATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgatcacaa ... tttatttcagGAACGTGAAAATCCAACTTTAACCG




















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: 67 (upstream exon), 66 (downstream exon)
Score: 25

CTTAAAACGGTGTAAACTCTCAGGGAATATATTCAACATCCTATTCAATCTCAACAAATTTATGGCATTTGAAACTCGTGATCCATTCCTCATTCGCCAGgtgatcacaa ... tttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgaattcactgttaatcatctaaataacaagttggatcatctttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
                       aaataac  putative branch site (score: 25)
                                      tcatctttttatttc  putative PPT
             ttaatcatctaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatcacaacttcttgccataaagcagtgaattcactgttaatcatctaaataacaagttggatcatctttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG