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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTAAAGGGGGTGGTTCTTTGGCCCCACCTTTCCCTTCTCCTTGCACCTTACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaactccgcctgatcaacctaccatattctttatgctaatatgttgtcctatgataatttgaccaatcctcgcttgatgtatctacaatag

Basic information

species Oryza sativa
transcript LOC_Os04g55960.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G104294_T02 (Zea mays), 5'ss of exon 4
TCGTAAAGGGGGTGGTTCTTTGGCCCCACCTTTCCCTTCTCCTTGCACCTTACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaactccgcctgatcaacctaccatattctttatgctaatatgttgtcctatgataatttgaccaatcctcgcttgatgtatctacaatag
||||||||| ||  |||| ||||||||||||||||| ||||| || || || |||||||| |||||| |||||||||||||||| ||| | || |||||||||| ||              || ||  |   | || |          || || | ||||  |||||| |||| | |  ||| ||    |    ||
TCGTAAAGGAGGAAGTTCCTTGGCCCCACCTTTCCCATCTCCATGTACTTTGCGGACTGCGCTTCTACGATATGCTGATCTACTCAATCCACCGAAGAAGgtccaca------------tgacttataagcattttca---------attttcttgtgatcgtttgactaatctttgaatgacgttatcatctcag

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G086489_T01 (Zea mays), 5'ss of exon 10
TCGTAAAGGGGGTGGTTCTTTGGCCCCACCTTTCCCTTCTCCTTGCACCTTACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaactccgcctgatcaacctaccatattctttatgctaatatgttgtcctatgataatttgaccaatcctcgcttgatgtatctacaatag
||||||||| || ||||| ||||||||||||||||| ||||| || ||||| |||||||| |||||| |||||||||||||||| ||| | || |||||||||| ||        ||||          ||| |||| |  |       |  | | ||||  ||||||||||| | |  |||||||   |    ||
TCGTAAAGGAGGAGGTTCCTTGGCCCCACCTTTCCCATCTCCATGTACCTTGCGGACTGCGCTTCTACGATATGCTGATCTACTCAATCCACCGAAGAAGgtccaca--------tgatttctaagaattatcctttctatt-------ttccttgtgattgtttgaccaatctttgaatgatgtaatcatctcag
















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|58676313|gb|CK065000.1|CK065000
EST:     TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAG                         GCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
genomic: TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaact ... tctacaatagGCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
EST: gi|29674048|gb|CB670323.1|CB670323
EST:     TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAG                         GCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
genomic: TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaact ... tctacaatagGCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
EST: gi|58661320|gb|CK050000.1|CK050000
EST:     TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAG                         GCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
genomic: TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaact ... tctacaatagGCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
EST: gi|33797029|gb|CF324379.1|CF324379
EST:     TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAG                         GCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
genomic: TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaact ... tctacaatagGCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
EST: gi|33676427|gb|CF304666.1|CF304666
EST:     TACGGACTGCACTTCTAACATATGCTGATCTACTTAATTCTCCAAAGAAG                         GCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
genomic: TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaact ... tctacaatagGCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
EST: gi|58695058|gb|CK083745.1|CK083745
EST:     TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAG                         GCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
genomic: TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaact ... tctacaatagGCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
EST: gi|88688747|gb|CI732323.1|CI732323
EST:     TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAG                         GCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
genomic: TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaact ... tctacaatagGCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
EST: gi|58681936|gb|CK070623.1|CK070623
EST:     AATTCTCCAAAGAAG                         GCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
genomic: AATTCTCCAAAGAAGgtcctcaact ... tctacaatagGCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
EST: gi|58655931|gb|CK044611.1|CK044611
EST:     TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAG                         GCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
genomic: TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaact ... tctacaatagGCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
EST: gi|2312399|gb|C28554.1|C28554
EST:     TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAG                         GCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
genomic: TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaact ... tctacaatagGCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
EST: gi|58654591|gb|CK043271.1|CK043271
EST:     TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAG                         GCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA
genomic: TACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaact ... tctacaatagGCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAA

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), 66 (downstream exon)
Score: 62

TCGTAAAGGGGGTGGTTCTTTGGCCCCACCTTTCCCTTCTCCTTGCACCTTACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaact ... tctacaatagGCTGCTTTGGTTGCTTTAGCTGCTCATGCGTCTGACCTAGCTGAAGCTGAAAGATTGAGATTTTTGGCTTCCCCTGCTGGAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTAAAGGGGGTGGTTCTTTGGCCCCACCTTTCCCTTCTCCTTGCACCTTACGGACTGCACTTCTAAGATATGCTGATCTACTTAATTCTCCAAAGAAGgtcctcaactccgcctgatcaacctaccatattctttatgctaatatgttgtcctatgataatttgaccaatcctcgcttgatgtatctacaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG