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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCAAGGCCCGCGCCGCCTGACCCCAACGACGCGAGGCAGCGGTTCTTGTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcgtttcacttggtttggatttcacctcgggtcattttattaggtttctgaaacaaattttgggtgatagcacatagctaacttcgtttcttc...

Basic information

species Oryza sativa
transcript LOC_Os07g07020.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07020.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 2
GAGGCAAGGCCCGCGCCGCCT---GACCCCAACGACGCGAGGCAGCGGTTCTTGTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcgtttcacttggtttggatttcacctcgggtcattttattaggtttctgaaacaaattttgggtgata-gcacatagctaacttcgtttcttc--------
   |  | |||  |||||      |||||  || | | ||| ||||| ||| |  | ||| | |||||| | |||||||||||||||||||||||||||||||||| |   |  | | |     |    ||||| |||     |  || || || ||    | | ||| |   ||   | |||  ||   ||| |  |    |         
---GGGAAGCCGCCGCCGTACAAGGACCCTGACAATGGGAGTCAGCGATTCCTACTCGAGTTGGAGTTCGTGCAGTGCCTCGCCAACCCTACCTACATCCACTgtactgtactgtcctccattctcttgtttcatctc-----accttgttgggatt----agctaatctgatgttgcacgcatctatagaacgttttcctgtaccggtttg

upper sequence: LOC_Os07g07020.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA10G38750.2 (Glycine max), 5'ss of exon 3
GAGGCAAGGCCCGCGCCGCCTGACCCCAACGACGCGAGGCAGCGGTTCTTGTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcgtttcacttggtttg--gatttcacctcgggtcattttattaggtttctgaaacaaattttgggtgatagcacatagctaacttcgtttcttc--
  | ||| |  |         || ||  | || | |  |||||| || ||| | ||  | |||||  | |||||||| ||||| |||||||||||||||||||    |      | ||| ||||  | ||||| ||    |||||  |  |  | |||| | |   |  | | ||  || |  |||    ||| |   |  |  
--GCCAAAGAACATATACAAAGATCCAGATGATGGGCAGCAGCGCTTTTTGCTTGAATTGGAGTTTGTTCAGTGCCTTGCCAATCCTACCTACATCCACTgtacgattttaactatttgatttgatggtttcagct----tcattgaacaaaatatctgcatctgttgattgttgcaagtaattagtgttctttgacacaacag

upper sequence: LOC_Os07g07020.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA20G28990.1 (Glycine max), 5'ss of exon 2
GAGGCAAGGCCCGCGCCGCCTGACCCCAACGACGCGAGGCAGCGGTTCTTGTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgta--attctcgtttcacttggtttggatttcacctcgggtcattttattaggtttctgaaacaaattttgggtgatagcacatagctaacttcgtttcttc----
  | ||| |  |         || ||  | || | |  ||||||||| ||| | ||  | |||||  | |||||||| ||||| |||||||||||||||||||  ||| ||  ||   || | |    ||||| ||    |||||  |  |  |  ||| | |   |  | | ||  || |  ||| |  ||| |   |  |    
--GCCAAAGAACATATACAAAGATCCAGATGATGGGCAGCAGCGGTTTTTGCTTGAATTGGAGTTTGTTCAGTGCCTTGCCAATCCTACCTACATCCACTgtatgattttcactttgatttgat--agtttcagct----tcattgaacaaaatacctgcatctgttgattgttgcaagtaattagttttctttgacacaacagct

upper sequence: LOC_Os07g07020.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ09598 (Selaginella moellendorffii), 5'ss of exon 1
-GAGGCAAGGCCCGCGCCGCCTGACCCCAACGACGCGAGGCAGCGGTTCTTGTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcgtttcacttggtttggatttcacctcgggtcattttattaggtttctgaaacaaattttgggtgatagcacatagctaacttcgtttcttc
  ||  | ||   | |  |   ||   | | |  | | ||||| | || ||||||||||| |||||| |||||||||| || || || |||||||| |||||||  | | ||||| | || ||||| |||    |||        |  | |||   ||   |   ||   |                              
TTAGCAATGGAGAGTGGTGAA-GAGGTCGATGGAGGGCGGCAGAGATTTTTGTTGGAGCTGGAGTTCGTCCAGTGCCTTGCAAATCCGACCTACATTCACTgtacgtattgtttc-cctgctttggctttgtgatcg-------ctgatgggtgattgttgccttttgcag------------------------------

upper sequence: LOC_Os07g07020.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ18119 (Selaginella moellendorffii), 5'ss of exon 1
-GAGGCAAGGCCCGCGCCGCCTGACCCCAACGACGCGAGGCAGCGGTTCTTGTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcgtttcacttggtttggatttcacctcgggtcattttattaggtttctgaaacaaattttgggtgatagcacatagctaacttcgtttcttc
  ||  | ||   | |  |   ||   | | |  | | ||||| | || ||||||||||| |||||| ||||||||||||| ||||| |||||||| |||||||  | | ||||| | || ||||| |||    |||        |  | |||   ||   |   ||   |                              
TTAGCAATGGAGAGTGGTGAA-GAGGTCGATGGAGGGCGGCAGAGATTTTTGTTGGAGCTGGAGTTCGTCCAGTGCCTCGCAAACCCGACCTACATTCACTgtacgtattgtttc-cctgctttggctttgtgatcg-------ctgatgggtgattgttgccttttgcag------------------------------

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|88569950|gb|CI661125.1|CI661125
EST:     GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTATCGGTTATCTCA
genomic: GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcg ... gttgaaacagATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTATCGGTTATCTCA
EST: gi|88337504|gb|CI630801.1|CI630801
EST:     GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTCTATCGGTTATCT
genomic: GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcg ... gttgaaacagATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTATCGGTTATCT
EST: gi|58602268|gb|CK012796.1|CK012796
EST:     GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTATC
genomic: GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcg ... gttgaaacagATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTATC
EST: gi|58609716|gb|CK037749.1|CK037749
EST:     GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTATCGGTTATCTCA
genomic: GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcg ... gttgaaacagATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTATCGGTTATCTCA
EST: gi|88348490|gb|CI629979.1|CI629979
EST:     GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACC-TACCTACATCCACT                         ATCTAGCGCAGAACAGATACTTTGAG
genomic: GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcg ... gttgaaacagATCTAGCGCAGAACAGATACTTTGAG
EST: gi|117250322|gb|CT843994.1|CT843994
EST:     GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACT                         ATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTATCGGTTATCTCA
genomic: GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcg ... gttgaaacagATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTATCGGTTATCTCA
EST: gi|88337564|gb|CI630861.1|CI630861
EST:     GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTAACTACATCCACT                         ATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTA
genomic: GTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcg ... gttgaaacagATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTA

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), 71 (downstream exon)
Score: 16

GAGGCAAGGCCCGCGCCGCCTGACCCCAACGACGCGAGGCAGCGGTTCTTGTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcg ... gttgaaacagATCTAGCGCAGAACAGATACTTTGAGGATGAGGCGTTTATCGGTTATCTCAAGTATCTCAAGTATTGGCAGCGTCCGGAGTACATCAAGTACATAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGCAAGGCCCGCGCCGCCTGACCCCAACGACGCGAGGCAGCGGTTCTTGTTGGAGCTCGAGTTCATCCAGTGCCTCGCCAACCCTACCTACATCCACTgtaattctcgtttcacttggtttggatttcacctcgggtcattttattaggtttctgaaacaaattttgggtgatagcacatagctaacttcgtttcttc

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa