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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggttactcttgtttgtatggtttttttggtaccatgtacaatgattgctgcttgatgatgcatgatttcatcttgacaagaacttttttgcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTACTGCGTCCTGGACGTCTAGACAGGAAGATTGAGATTCCGCTACCAAATG

Basic information

species Oryza sativa
transcript LOC_Os02g10640.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G171604_T01 (Zea mays), 3'ss of exon 7
tggttactcttgtttgtatggtttttttggt-accatgtacaatgattgctg-cttgatgatgcatgatttcatcttgacaagaacttttttgcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTACTGCGTCCTGGACGTCTAGACAGGAAGATTGAGATTCCGCTACCAAATG
     | | ||    ||    ||| | || |       || ||    |  || |||| |  || |||| || |  |||||||| |  ||||  | | ||||||| || ||||||||||| || ||| ||||||||||||||||||||||||| ||||||||||||||| |||||||||||||||| ||||||||||| || |
--cacaatatttaccgtgcattttctatgattgttgcatagaacagcttgtgtcttgtttctgtatgagtttagtttgacaaggatattttgacctgaacagGTAAAGATGATCATGGCCACGAATCGACCTGATGTTCTGGACCCTGCGCTCCTGCGTCCTGGACGTTTAGACAGGAAGATTGAAATTCCGCTACCCAACG

upper sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G165817_T01 (Zea mays), 3'ss of exon 7
------tggttactc---ttgtttgtatggtttttttggtaccatg-tacaatgattgctgc----ttgatgatgcatgatttcatcttgacaagaacttttttgcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTACTGCGTCCTGGACGTCTAGACAGGAAGATTGAGATTCCGCTACCAAATG
      | |||| |    ||  |   ||  |||| | ||||| | | || | |   |  ||     ||| |  ||  | | ||||  |||||||| |  |||| |||| ||||||| |||||||||||||| || ||| ||||||||||||||||||| ||||| ||||||||||||||| |||| ||||||||||| ||||||||||| || |
gtaaatttgttatttggattactcacatt-ttttctaggtacaacgatatagtagcttgtgtcttgttgtttctgtctaaattcagtttgacaaggatattttggcttgaacagGTAAAAATGATCATGGCCACAAATCGACCTGATGTTCTGGACCCGGCGCTCCTGCGTCCTGGACGTTTAGATAGGAAGATTGAAATTCCGCTACCCAACG

upper sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S91_182V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------tggttactcttgtttgtatggtttttttggtaccatgtacaatgattgctgcttgatgatgcatgatttcatcttg-acaagaacttttttgcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTACTGCGTCCTGGACGTCTAGACAGGAAGATTGAGATTCCGCTACCAAATG
                            |  | |     |    |||||||  | ||  |   | |   | | |   ||   |   ||   |  | |||| ||  ||| | ||      |   | |||||| || ||||||||||| |||||| ||||||||||||| ||||||||  | || || || || ||| ||||  | |||||||| ||||| ||||||||||
gtgtgttaagattctgaatctatcctagtaataatagcagacactatggttactctgaaattttttgtcacg-tgcatggcagccaatatcttgtctcatttttcacatgtacc-----gaggatacagGTAAAGATGATCATGGCAACCAATCGACCTGATGTTCTTGACCCTGCATTGCTCCGACCCGGCCGTTTAGATCGAAAGATTGAAATTCCACTACCAAATG

upper sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ28962 (Selaginella moellendorffii), 3'ss of exon 7
tggttactcttgtttgtatggtttttttggtaccatgtacaatgattgctgcttgatgatgcatgatttcatcttgacaaga-acttttttgcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTACTGCGTCCTGGACGTCTAGACAGGAAGATTGAGATTCCGCTACCAAATG
                                                     |   |||  |   ||||   |   | | | | ||     |||   |||||||||||||||||||| ||||| ||||| |||||  |||| || ||||| ||| | ||||| ||| | ||| | ||||| ||||||||| | || || |
----------------------------------------------------gtagggattgaaagtttctcatgttctatatagttggcctcttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTCCTGAGACCTGGTCGTTTGGACCGAAAGATCGAGATTCCGTTGCCCAACG

upper sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ13668 (Selaginella moellendorffii), 3'ss of exon 7
tggttactcttgtttgtatggtttttttggtaccatgtacaatgattgctgcttgatgatgcatgatttcatcttgacaagaacttttttgcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTACTGCGTCCTGGACGTCTAGACAGGAAGATTGAGATTCCGCTACCAAATG
                                                    | |    || | ||||      |   |   | ||     |||   |||||||||||||||||||| ||||| ||||| |||||  |||| || ||||| ||| | ||||| ||| | ||| | ||||| ||||||||| | || ||||
---------------------------------------------------gtagggattggaagattctcatgttctatatagttggcctcttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTCCTGAGACCTGGTCGTTTGGACCGAAAGATCGAGATTCCGTTGCCCAATG

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|163917943|gb|EG715243.1|EG715243
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|58686072|gb|CK074759.1|CK074759
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGANCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|300215978|gb|HO088604.1|HO088604
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|218493541|gb|FG956814.1|FG956814
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|218480375|gb|FG953360.1|FG953360
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|396941346|gb|HO188555.1|HO188555
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|8955808|gb|BE229613.1|BE229613
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|218501848|gb|FG946073.1|FG946073
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|25778017|gb|CA752769.1|CA752769
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|33795428|gb|CF323584.1|CF323584
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|218486211|gb|FG960168.1|FG960168
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|58662318|gb|CK050998.1|CK050998
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCAT
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCAT
EST: gi|27577669|gb|CB000364.1|CB000364
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|58587300|gb|CF985608.1|CF985608
EST:     CAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|55408414|gb|CV720790.1|CV720790
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|58587845|gb|CF986153.1|CF986153
EST:     GAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCGTGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
genomic: GAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTA
EST: gi|86829542|gb|CI286737.1|CI286737
EST:     CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAG                         GTGAAAATGATCATGGCTACCAATAGACCTG
genomic: CACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTG

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), 75 (downstream exon)
Score: 57

TGGGCGGCGGTTCAGTGAAGGAACTAGTGCTGATCGCGAGATCCAGCGCACACTGATGGAACTGCTAAATCAGTTAGATGGATTTGATGAACTTGGAAAGgtaacttatt ... gcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTACTGCGTCCTGGACGTCTAGACAGGAAGATTGAGATTCCGCTACCAAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgcttgatgatgcatgatttcatcttgacaagaacttttttgcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTACTGCGTCCTGGACGTCTAGACAGGAAGATTGAGATTCCGCTACCAAATG
                          tcttgac  putative branch site (score: 57)
                                      cttttttgctt  putative PPT
                                    aactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggttactcttgtttgtatggtttttttggtaccatgtacaatgattgctgcttgatgatgcatgatttcatcttgacaagaacttttttgcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTACTGCGTCCTGGACGTCTAGACAGGAAGATTGAGATTCCGCTACCAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - tgtttgt
- - - - - - - - - - - - - - - - -catgtac
- - - - - - - - - - - - - - - - - - - - - - - tgctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagaac