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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcaccattttctcttgttttatcccttttctttatttcttgtctttctaagtaattgtgatcagcagaactcttctctagattatagttgattattttttttgttcaaatcatatttttacagtggctaaaacttctgctaacag

Basic information

species Oryza sativa
transcript LOC_Os06g40650.4
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40650.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G345544_T02 (Zea mays), 5'ss of exon 6
GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcaccattttctcttgttttatcccttttctttatttcttgtctttctaagtaattgtgatcagcagaactcttctctagattatagttgattattttttttgttcaaatcatatttttacagtggctaaaacttctgctaacag
|||| |||||||| || |||||||| || ||||||||||| ||||| ||||||||||||||||| |||||||||||||||||||| || |||||||||||  |  |  |  |  || | |||| |   | |  |   | |  | ||||   |   | | |   |||||||||||||| |||||       | ||  |||||  |||| |  ||| | |||| ||  ||| ||||||||||||||    
GACCTACATCTTTCGCTCCGATGATCGAGACAGCAATTGGAATTGTTGACAGCACTGGTGGTCAATATCATGTTCTTCTGATAATCGCAGATGGACAGgttggcgaatacatggtcattttttttgtttctgttgcctgttatttcttatcattaagtggctgtcagcagaactcttttctag-------tggaacattttggttgtcc--atccttttttcact-tggataaaacttctgctag---

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G071659_T01 (Zea mays), 5'ss of exon 6
GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcaccattttctc---ttgttttatcccttttctttatttcttgtctttctaagtaatt--gtgatcagcagaactcttctctagattatagttgattattttttttgttcaaatcatatttttacagtggctaaaacttctgctaacag
|||| ||||||||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||| |||||||||||||||||||| ||||||||||||||  || |  |  || ||   |||| ||  || |  | ||  |  | |||  ||     | |||  ||| |   ||| |    ||| |    | ||||  |  |||||  ||||    ||| | |||| ||  ||| ||||||||||| |   ||
GACCTACATCTTTTGCGCCGATGATTGAGACAGCAATTGGAATTGTTGACAGCACTGGTGGTCAATATCATGTTCTTCTGATAATCGCCGATGGACAGgttggtgaatacattgtcattttgtctttgccttcgttttagtcacctgttatttcttatcattaagtggttgccagcaaagctcttt----tctagtgcaacattttgattgtct--atccttttttcact-tggataaaacttctggttctag

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv00s0780g00040.t01 (Vitis vinifera), 5'ss of exon 6
GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcaccattttctcttgttttatcccttttctttatttcttgtctttctaagtaattgtgatcagcagaactcttctctagattatagttgattattttttttgttcaaatcatatttttacagtggctaaaacttctgctaacag
||||||| |||||||| || || || ||||| || ||||  ||||| |||| || |||||||||||| ||||||||| |||| || || ||||| |||||| ||    |  |   | | | | | |  |||  || ||||   || ||||    |   | |||  ||  |   | | | |   |||    | | ||  |   | || | |      |||   |||     |  ||             
GACCAACTTCTTTTGCTCCCATAATAGAAACTGCTATTGAAATTGTGGACACCAGTGGTGGTCAGTACCATGTTCTTGTGATTATTGCTGATGGGCAGgtcagttgttaaatatgcatttatcaactgttt--ttaatttggcgtttttcggttttcctctgactag--ggtttttacccattatttccatggctttctgagtctgat-atgcttgattccaacacaatatgcaag------------

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|116875559|gb|EC366067.1|EC366067
EST:     ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAG                         GTTACTCGAAGTGTTGATACGCAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
genomic: ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcacc ... ctgctaacagGTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
EST: gi|58692386|gb|CK081073.1|CK081073
EST:     ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAG                         GTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
genomic: ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcacc ... ctgctaacagGTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
EST: gi|66928286|gb|CX115134.1|CX115134
EST:     ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAG                         GTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
genomic: ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcacc ... ctgctaacagGTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
EST: gi|29632713|gb|CB637722.1|CB637722
EST:     ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAG                         GTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
genomic: ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcacc ... ctgctaacagGTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
EST: gi|300216150|gb|HO087935.1|HO087935
EST:     ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAG                         GTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
genomic: ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcacc ... ctgctaacagGTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
EST: gi|58695004|gb|CK083691.1|CK083691
EST:     ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAG                         GTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
genomic: ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcacc ... ctgctaacagGTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
EST: gi|125863438|gb|EL586714.1|EL586714
EST:     ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAG                         GTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
genomic: ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcacc ... ctgctaacagGTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
EST: gi|116875525|gb|EC366033.1|EC366033
EST:     ACAGCACTGGTGGTCGGTATCATGTTCTTCTGATAATAGCCGATGGACAG                         GTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
genomic: ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcacc ... ctgctaacagGTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
EST: gi|58678137|gb|CK066824.1|CK066824
EST:     ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAG                         GTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT
genomic: ACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcacc ... ctgctaacagGTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGT

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), 70 (downstream exon)
Score: 68

GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcacc ... ctgctaacagGTTACTCGAAGTGTTGATACACAGTCTGGGCAGTTAAGCCCGCAGGAGCGTGATACGATTGATGCTATAGTAAAAGCTAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCAACATCTTTTGCCCCGATGATTGAAACAGCAATTGGTATTGTAGACAGCACTGGTGGTCAGTATCATGTTCTTCTGATAATAGCCGATGGACAGgtctgtcaccattttctcttgttttatcccttttctttatttcttgtctttctaagtaattgtgatcagcagaactcttctctagattatagttgattattttttttgttcaaatcatatttttacagtggctaaaacttctgctaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA