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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgaagcgttgaaatgctaggctttaacatactaacattacatagttctgtttaattaacatatggtagaactgacctatttgggatatatttctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGAGATCCTGTGCAGAAGGCTGAAGCAATGGCTTTTCGCCGAGCTTGTACCC

Basic information

species Oryza sativa
transcript LOC_Os01g65560.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G120814_T03 (Zea mays), 3'ss of exon 3
-tcgaagcgttgaaatgctaggctttaacatactaacattacatagttctgtttaattaacatatggtagaactgacctatttgggatatatt-tctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGAGATCCTGTGCAGAAGGCTGAAGCAATGGCTTTTCGCCGAGCTTGTACCC
| | | | ||| ||| | || | | || || ||| | ||| | | | ||| | | | || ||| ||||||||| ||||| |||||||||||| |||||| |||||||||| |||||| ||||| || |||||||| ||| | ||||||||||| || |||||| | |
gacaatttctctgcctagtag-ttttgtctaacatataatatatgaccaaaactaac-agtgtattgacaatgttgcctgctctctctgttttctctatcagATCTATAGAGAGGCCACTGGAACTGCTTCTGTTGATGATACAATCTATGGTGATCCCGTACAGAAGGCAGAATCTATGGCTTTTCGTCGCGCTTGTGCGC

upper sequence: LOC_Os01g65560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G005061_T03 (Zea mays), 3'ss of exon 1
-tcgaagcgttgaaatgctaggctttaacatacta-acattacatagttctgtttaattaacatatggtagaactgacctatttgggatatatt-tctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGAGATCCTGTGCAGAAGGCTGAAGCAATGGCTTTTCGCCGAGCTTGTACCC
|| || | | | | | ||||||||| | | || | ||| || ||| | | | | || | | | | ||| ||||||||| ||||| || ||||||||| |||||| |||||||||| ||||||| ||||| | |||||||| ||||| ||||||||||| || |||||| | |
ttctgagtgcagtagttttg---tttaacatataatatatgatcagaactaacataaatagtgtattgacaatgttatctgctctctctgttctctctatcagATCTATAGAGAGGCTACTGGAACTGCTTCTGTTGATGATACAAGCTATGGTGATCCCATACAGAAGGCAGAAGCTATGGCTTTTCGTCGTGCTTGTGCAC

upper sequence: LOC_Os01g65560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G36860.1 (Glycine max), 3'ss of exon 3
tcgaagcgttgaaatgctag--gctttaacatactaaca---ttacatagttctgtttaattaacatatggtagaactgacctatttgggatatatttctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGAGATCCTGTGCAGAAGGCTGAAGCAATGGCTTTTCGCCGAGCTTGTACCC
|| || | ||| | | || | | || || || |||||| || ||| | | | || | | || | || ||||||| | |||| | || ||| | ||||| ||| |||| | || || ||| | |||||||||||||| |||||||| ||||||||||||||||| |||||||| | |
-gaaaatgtagttatggtgattgagttggaaaattagcagattttgttagttcctcttcattc-tgtcttattgacccgg--taagtcccatttatttctct-agATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGAGATCCTGTACAGAAGGCAGAAGCAATGGCTTTTCGTAGAGCTTGTGCAC

upper sequence: LOC_Os01g65560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G71310.1 (Arabidopsis thaliana), 3'ss of exon 3
tcgaagcgttgaaatgctaggctttaacatactaacattacatagttctgtttaattaacatatg-gtagaactgacctatttgggat-atatttct-------ttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGAGATCCTGTGCAGAAGGCTGAAGCAATGGCTTTTCGCCGAGCTTGTACCC
| || || ||| | |||| || || ||| ||| || || |||| | | | ||| | | | | || || ||| | | |||| | || ||| | || || || | |||| ||||| | ||||||||| ||| ||||||| ||||| ||||||||||| |||||||| || ||| |
------tccttgcatacttt-cttgagcatattatgttttcattgttttgcttg--taacttgtacgctgaaatcatttgctaataatcatttttttggtgttgtcaagATATTTAGGGAATCAACAGGTACCACATCTGTAGATGACAAAGGCTATGGTGATGCTGTGCAAAAGGCGGAAGCAATGGCATTTCGCCGTGCGTGTGCAA

upper sequence: LOC_Os01g65560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0089g00930.t01 (Vitis vinifera), 3'ss of exon 3
-tcgaagcgttgaaatgctaggctttaacatactaacattacatagttctgtttaattaacatatggtagaactgacct--atttgggatatatttctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGAGATCCTGTGCAGAAGGCTGAAGCAATGGCTTTTCGCCGAGCTTGTACCC
| | | | || || || || | || | ||| || || | | ||| || || | | | | |||| ||||| |||||||| | || |||||| ||| | || || |||||||||||||||||||| |||||||| |||||||||||||| | || |||||| | |
catcagctactttgttttttatctcaaaaatgaaaagaggccaaacccctg---aaggaaaactaacttgaattgcccgtaacattatttgtctttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGAGATCCTGTACAGAAGGCGGAAGCAATGGCTTTCAGGCGTGCTTGTGCAC

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|86846949|gb|CI283080.1|CI283080
EST:     AATCTGTATCTGTTATTTATCGCGTGACTCTCCATGGAACTGATGCAGAG                         ATCTACAGAGAAGCCACTGGAACCTCTTCTGCTGATGATACAGGCTATGGA
genomic: AATCTGTATCTGTTATTTATCGCGTGACTCTCCATGGAACTGATGCAGAGgtacctattt ... tttctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGA
EST: gi|86424264|gb|CI063025.1|CI063025
EST:     AATCTGTATCTGTTATTTATCGCGTGACTCTCCATGGAACTGATGCAGAG                         ATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGA
genomic: AATCTGTATCTGTTATTTATCGCGTGACTCTCCATGGAACTGATGCAGAGgtacctattt ... tttctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGA
EST: gi|88203245|gb|CI203094.1|CI203094
EST:     AATCTGTATCTGTTATTTATCGCGTGACTCTCCATGGAACTGATGCAGAG                         ATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGA
genomic: AATCTGTATCTGTTATTTATCGCGTGACTCTCCATGGAACTGATGCAGAGgtacctattt ... tttctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGA

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: 38 (upstream exon), 31 (downstream exon)
Score: 5

AATGGTCTGGCGAGGTTCGCAGCATTGTTTATTCATCTGATGGAAAATCTGTATCTGTTATTTATCGCGTGACTCTCCATGGAACTGATGCAGAGgtacctattt ... tttctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGAGATCCTGTGCAGAAGGCTGAAGCAATGGCTTTTCGCCGAGCTTGTACCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtttaattaacatatggtagaactgacctatttgggatatatttctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGAGATCCTGTGCAGAAGGCTGAAGCAATGGCTTTTCGCCGAGCTTGTACCC
                        aactgac  putative branch site (score: 5)
 tatttctttc  putative PPT
 tttaattaacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgaagcgttgaaatgctaggctttaacatactaacattacatagttctgtttaattaacatatggtagaactgacctatttgggatatatttctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGAGATCCTGTGCAGAAGGCTGAAGCAATGGCTTTTCGCCGAGCTTGTACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - -aaatgct
- - - - - - - - - - - - - - - actaaca