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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgcgaacccttgtgt...

Basic information

species Oryza sativa
transcript LOC_Os07g42950.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G054136_T01 (Zea mays), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattct-cgccgccgctc--ccccgt-ttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgcgaacccttgtgt
|||||||||||||||||  ||||||||||||| |||||||| || |||||||||||||||||||||||||| ||   || |  |  ||  | | || || ||||||||| |  | ||  | | ||||||||||  | |   | |||| | |    |       | ||| 
TTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCTgtgagtgtttcgcgtcctccatctgctctgtattttttcgtttctcttagatctgtgggagtggtgtt--ttgcttcgagcccactt--tgtagctgatggtgc

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G851698_T01 (Zea mays), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattct-cgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggt--agtggcaagccgaatcagcgcgaacccttgtgt
|||||||||||||||||| | |||||||||||||||||||| || ||||||||||||||||| |||||||| |||  |    ||  |   |  | | |||  | || |  | ||    | ||||||||||     ||  ||    || | | |     |      |  
TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACTgtgagtgttcgacattccctatttgctctgtatttt-tgtctcttagatccatgtgagtggtgttctctcagatgctcttcgtagctgttgttaagacgat--

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G054136_T02 (Zea mays), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattct-cgccgccgctc--ccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgcgaacccttgtgt-
|||||||||||||||||  ||||||||||||| |||||||| || |||||||||||||||||||||||||| ||   || |  |  ||  | | || | ||||||||| |  | ||  | | ||||||||||  | |   | |||| | |    |       | |||  
TTCAACATCGCGAACCCTTCCACCGGGTGCCAAAAGAAGCTGGAAATCGATGACGACCAGAAGCTgtgagtgtttcgcgtcctccatctgctctgtatttttcgtttctcttagatccgtgggagtggtgtt--ttgcttcgagcccactt--tgtagctgatggtgcc

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA18G26190.1 (Glycine max), 5'ss of exon 1
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgcgaacccttgtgt------
|||||||||||||  || ||||| || ||||||||||||||||||||||| ||||| ||||| |||| |  | | || |     ||  |    || ||| | |     | | ||     ||||  |  |  | ||     |  |  |  | | |      | ||       
TTCAACATCGCGAGTCCCACCACTGGATGCCAGAAGAAGCTCGAGATCGACGACGATCAGAAACTgtaatcact-tcactctttctttctttctttttttggtgttaaattttt-----gagtatttctacttgttcttcgtggtgttcgtgtgttgtgctttgagagaaa

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA15G08210.1 (Glycine max), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgcgaacccttgtgt--
|||||||| ||||| || ||||| || || ||||||||||| ||||||||||| |||| |||||||| | | |  ||  | ||  |      ||   ||  ||      |||    ||| |    ||      || | |     ||||        |  |  |||  
TTCAACATTGCGAATCCCACCACTGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaatt-tcatcttcaccattttaattttccattacttgtgttcatag-gaagaaataaatgaaaaatgtcggagttttaatctattttccctttgttgtgt

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA13G31130.1 (Glycine max), 5'ss of exon 3
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgcgaacccttgtgt
|||||||| ||||| || |||||||| || ||||||||||| ||||||||||| |||| |||||||| ||| ||| |        |  ||||||  || ||||      |    | | |      | |  | | |   || |    |   |         |   |
TTCAACATTGCGAATCCCACCACCGGTTGTCAGAAGAAGCTGGAGATCGATGATGACCTGAAGCTgtaagttttcaccattttattttcccgttacttgcgttcataggaagaaataaatgaaaatttccgaaattttaatctattttccctttgttgtgtaatt

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA13G24630.1 (Glycine max), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgcgaacccttgtgt----
|||||||| || || || ||||| ||||||||||||||||| || ||||||||||||| |||||||| |  ||| || |   | || |    ||  |||   || | |    |  ||  | |||  ||  || |||   ||  |||  | ||       ||  ||    
TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCTgtaatcatt-tcactttctctgcaattttcatttgtattactct---tctgattgtgtgtcgtgtgttgtgcttagaggaaaaaccgttgctttttaagtgggg

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA07G31840.2 (Glycine max), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgttt-cgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgcgaacccttgtgt-
|||||||| || || || ||||| ||||||||||||||||| || ||||||||||||| |||||||| |  ||| || |   | || |    ||  |||   |  | |   |  | | | |  | |||||| |  |   |||   ||||    |        | |  
TTCAACATTGCAAATCCCACCACTGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCTGAAGCTgtaatcatt-tcactctctcttcaattttcatttgtatcactcttctgatcgcgtgtcttgtgttg-tgcttagaagaaaaatcgttactttaaagcgggga

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G45770.1 (Glycine max), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgcgaacccttgtgt-
|||||||||||||| || ||||| || ||||||||||||||||||||||| ||||| | ||| |||| | |||| || |      |      | |      ||||     | |    |    ||||| || | |||    |     |||  |  |     | | | 
TTCAACATCGCGAATCCCACCACTGGATGCCAGAAGAAGCTCGAGATCGACGACGATCTGAAACTgtaattatt-tcactcttttttttaattataaaatatttcgtatttctacttgttcttggtggtgttcgtgtgttgtgctttcaaagaaagttgatttatt

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G10360.1 (Arabidopsis thaliana), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtt-tcgtttccccaatattagagagagtg-gtgttggtagtgg-caagccg--aatcagcgcgaacccttgtgt
|||||| |||| || |||||||||||||| || ||||| ||||||||||||||||| || || |||| || ||  | ||      || |   ||  |  | | ||     | ||| |    | || |||| |   |||  ||| | |  |   ||  || |   ||    
TTCAACGTCGCCAATCCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACTgtaag-atctttgctttaaatcacattttcttcatggatttgtttacatttggcttattgagtgtagagtgtgaacaatctgctatgaagttcgtaaaatt----

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgcgaacccttgtgt
|||||| | ||||| || || || || ||||||||||||||||||||||| || |||||||| |||| ||  ||  |  | | | | |  | |   |    |||     |||||         | ||   |   |    |   |  |  |     | |  |||  
TTCAACGTTGCGAATCCAACTACTGGATGCCAGAAGAAGCTCGAGATCGACGATGACCAGAAACTgtaagattttgcttctctgtttcatcttcattcatttttaatagatatttcgtgctaggttgccagatctattgattggtgtttgtatatatcactgtta

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtg-ttggtagtggcaagccgaatcagcgcgaacccttgtgt-
||||| |||||||| |||||||| || |||||||||||||| ||||| || || |||||||| |||| |||  |  |             |   | | | | ||    |||||  ||  || |  |  |||||  ||          |     |   |  |  |   
TTCAATATCGCGAATCCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgcttacttgattcagtgttctcatatatggatta--aaatatgtgattgaatcattcttggttttgttgcttttctttctttctttctttctttct

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgcgaacccttgtgt--
||||| ||||| || || || || || || ||||||||||||||||| |||||||| ||||| |||| ||  |||      || |       |||  ||| | | |    | ||   ||||    || | | | |    ||   |    |    |    || | |  
TTCAATATCGCAAATCCTACTACAGGATGTCAGAAGAAGCTCGAGATTGATGACGATCAGAAACTgtaagctttcaaattcccacgttttt-ttttcttcctatgcgttttgttgctgagaa-aatgatagaaattattagttaatgttgttttaggttttttttcc

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S253_7V6.1 (Physcomitrella patens), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgc---gaacccttgtgt
 |||||||||| ||||| ||||| |||||||| |||||| | |||||||||||||||   ||||||| |||    | |   ||     ||  ||   |  |       | | |      |  |  |    | | |          ||| |||    | || ||| |  
CTCAACATCGCCAACCCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgcttggttccctgcgacctcttcagtcagacggtggattgtcgctttggattttacgtgcactcttgt-ttatatctgcgttttgcactctttt--

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S31_322V6.1 (Physcomitrella patens), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccga-atcagcgcgaacccttgtgt
 |||| ||||| || || ||||| ||||||||||||||| |||||||||||||||||   |||||||||||| |  |||               |||  |||   |  ||| ||         ||    |||    | | |   | || || |   |    || ||
CTCAATATCGCTAATCCCACCACAGGGTGCCAGAAGAAGGTCGAGATCGATGACGACGCTAAGCTgtgagtagtgccgcaatgctgtttgtcaatgtgccgtgggcttaatgttgttttataagggtccggtcacagtacgagaatattagggtttagtgctg-gt

upper sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S253_38V6.1 (Physcomitrella patens), 5'ss of exon 2
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagc-cgaatcagcgcgaacccttgtgt
 |||||||||| ||||| || || ||||||||||||||| | |||||||||||||||   ||||||| |||    | |          ||| ||    ||  |      || || |   |     | |  ||  |  |  |  ||   | |||     |  ||  |
CTCAACATCGCCAACCCCACTACGGGGTGCCAGAAGAAGGTTGAGATCGATGACGACGCTAAGCTgtaagtggcttggttctttgcgaccctttgcagtctgtcggtggatgttcgcctgca-attttacgtgctctcttgttcgcgcctgcgttttgcactgctt

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|29682891|gb|CB679166.1|CB679166
EST:     CCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCT                         GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCT
genomic: CCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattc ... tgtactgcagGCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCT
EST: gi|58675684|gb|CK064371.1|CK064371
EST:     GAGATCGATGACGACCAGAAGCT                         GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCGGTGGCGATGCTCT
genomic: GAGATCGATGACGACCAGAAGCTgtgagtattc ... tgtactgcagGCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCT
EST: gi|58605263|gb|CK033296.1|CK033296
EST:     CCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCCGAAGCT                         GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCT
genomic: CCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattc ... tgtactgcagGCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCT
EST: gi|58680867|gb|CK069554.1|CK069554
EST:     CCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCT                         GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCT
genomic: CCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattc ... tgtactgcagGCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCT
EST: gi|218490056|gb|FG943987.1|FG943987
EST:     CCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCT                         GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCT
genomic: CCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattc ... tgtactgcagGCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCT
EST: gi|218494399|gb|FG963390.1|FG963390
EST:     CCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCT                         GCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCT
genomic: CCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattc ... tgtactgcagGCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCT

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), 58 (downstream exon)
Score: 186

TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattc ... tgtactgcagGCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtttcgtttccccaatattagagagagtggtgttggtagtggcaagccgaatcagcgcgaacccttgtgt

- - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccgccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccccc